Proteomics data analysis: heart

1 Background

Researchers have assessed the proteome in different regions of the heart for 3 patients (identifiers 3, 4, and 8). For each patient they sampled the left atrium (LA), right atrium (RA), left ventricle (LV) and the right ventricle (RV). The data are a small subset of the public dataset PXD006675 on PRIDE.

Suppose that researchers are mainly interested in comparing the ventricular to the atrial proteome. Particularly, they would like to compare the left atrium to the left ventricle, the right atrium to the right ventricle, the average ventricular vs atrial proteome and if ventricular vs atrial proteome shifts differ between left and right heart region.

2 Data

We first import the peptides.txt file. This is the file that contains your peptide-level intensities. For a MaxQuant search [6], this peptides.txt file can be found by default in the “path_to_raw_files/combined/txt/” folder from the MaxQuant output, with “path_to_raw_files” the folder where raw files were saved. In this tutorial, we will use a MaxQuant peptides file from MaxQuant that can be found in the data tree of the SGA2020 github repository https://github.com/statOmics/SGA2020/tree/data/quantification/heart .

To import the data we use the QFeatures package.

We generate the object peptideRawFile with the path to the peptideRaws.txt file. Using the grepEcols function, we find the columns that contain the expression data of the peptideRaws in the peptideRaws.txt file.

library(tidyverse)
library(limma)
library(QFeatures)
library(msqrob2)
library(plotly)

peptidesFile <- "https://raw.githubusercontent.com/statOmics/PDA21/data/quantification/heart/peptides.txt"

ecols <- grep("Intensity\\.", names(read.delim(peptidesFile)))

pe <- readQFeatures(
  table = peptidesFile,
  fnames = 1,
  ecol = ecols,
  name = "peptideRaw", sep="\t")

pe

## An instance of class QFeatures containing 1 assays:
##  [1] peptideRaw: SummarizedExperiment with 31319 rows and 12 columns

pe[["peptideRaw"]]

## class: SummarizedExperiment 
## dim: 31319 12 
## metadata(0):
## assays(1): ''
## rownames(31319): AAAAAAAAAK AAAAAAAAEQQSSNGPVK ... YYTPVPCESATAK
##   YYTYLIMNK
## rowData names(91): Sequence N.term.cleavage.window ...
##   Oxidation..M..site.IDs MS.MS.Count
## colnames(12): Intensity.LA3 Intensity.LA4 ... Intensity.RV4
##   Intensity.RV8
## colData names(0):

We will make use from data wrangling functionalities from the tidyverse package. The %>% operator allows us to pipe the output of one function to the next function.

colData(pe)$location <- substr(
  colnames(pe[["peptideRaw"]]),
  11,
  11) %>%
  unlist %>%  
  as.factor

colData(pe)$tissue <- substr(
    colnames(pe[["peptideRaw"]]),
    12,
    12) %>%
    unlist %>%  
    as.factor

colData(pe)$patient <- substr(
  colnames(pe[["peptideRaw"]]),
  13,
  13) %>%
  unlist %>%  
  as.factor

We calculate how many non zero intensities we have per peptide and this will be useful for filtering.

rowData(pe[["peptideRaw"]])$nNonZero <- rowSums(assay(pe[["peptideRaw"]]) > 0)

Peptides with zero intensities are missing peptides and should be represent with a NA value rather than 0.

pe <- zeroIsNA(pe, "peptideRaw") # convert 0 to NA

2.1 Data exploration

63% of all peptide intensities are missing and for some peptides we do not even measure a signal in any sample. The missingness is similar across samples.

3 Preprocessing

This section preforms standard preprocessing for the peptide data. This include log transformation, filtering and summarisation of the data.

3.1 Log transform the data

pe <- logTransform(pe, base = 2, i = "peptideRaw", name = "peptideLog")
limma::plotDensities(assay(pe[["peptideLog"]]))

3.2 Filtering

3.2.1 Handling overlapping protein groups

In our approach a peptide can map to multiple proteins, as long as there is none of these proteins present in a smaller subgroup.

pe <- filterFeatures(pe, ~ Proteins %in% smallestUniqueGroups(rowData(pe[["peptideLog"]])$Proteins))

3.2.2 Remove reverse sequences (decoys) and contaminants

We now remove the contaminants, peptides that map to decoy sequences, and proteins which were only identified by peptides with modifications.

First look to the names of the variables for the peptide features

pe[["peptideLog"]] %>%
  rowData %>%
  names

##  [1] "Sequence"                "N.term.cleavage.window" 
##  [3] "C.term.cleavage.window"  "Amino.acid.before"      
##  [5] "First.amino.acid"        "Second.amino.acid"      
##  [7] "Second.last.amino.acid"  "Last.amino.acid"        
##  [9] "Amino.acid.after"        "A.Count"                
## [11] "R.Count"                 "N.Count"                
## [13] "D.Count"                 "C.Count"                
## [15] "Q.Count"                 "E.Count"                
## [17] "G.Count"                 "H.Count"                
## [19] "I.Count"                 "L.Count"                
## [21] "K.Count"                 "M.Count"                
## [23] "F.Count"                 "P.Count"                
## [25] "S.Count"                 "T.Count"                
## [27] "W.Count"                 "Y.Count"                
## [29] "V.Count"                 "U.Count"                
## [31] "O.Count"                 "Length"                 
## [33] "Missed.cleavages"        "Mass"                   
## [35] "Proteins"                "Leading.razor.protein"  
## [37] "Start.position"          "End.position"           
## [39] "Gene.names"              "Protein.names"          
## [41] "Unique..Groups."         "Unique..Proteins."      
## [43] "Charges"                 "PEP"                    
## [45] "Score"                   "Identification.type.LA3"
## [47] "Identification.type.LA4" "Identification.type.LA8"
## [49] "Identification.type.LV3" "Identification.type.LV4"
## [51] "Identification.type.LV8" "Identification.type.RA3"
## [53] "Identification.type.RA4" "Identification.type.RA8"
## [55] "Identification.type.RV3" "Identification.type.RV4"
## [57] "Identification.type.RV8" "Fraction.Average"       
## [59] "Fraction.Std..Dev."      "Fraction.1"             
## [61] "Fraction.2"              "Fraction.3"             
## [63] "Fraction.4"              "Fraction.5"             
## [65] "Fraction.6"              "Fraction.7"             
## [67] "Fraction.8"              "Fraction.100"           
## [69] "Experiment.LA3"          "Experiment.LA4"         
## [71] "Experiment.LA8"          "Experiment.LV3"         
## [73] "Experiment.LV4"          "Experiment.LV8"         
## [75] "Experiment.RA3"          "Experiment.RA4"         
## [77] "Experiment.RA8"          "Experiment.RV3"         
## [79] "Experiment.RV4"          "Experiment.RV8"         
## [81] "Intensity"               "Reverse"                
## [83] "Potential.contaminant"   "id"                     
## [85] "Protein.group.IDs"       "Mod..peptide.IDs"       
## [87] "Evidence.IDs"            "MS.MS.IDs"              
## [89] "Best.MS.MS"              "Oxidation..M..site.IDs" 
## [91] "MS.MS.Count"             "nNonZero"

No information on decoys.

pe <- filterFeatures(pe,~ Potential.contaminant != "+")

3.2.3 Drop peptides that were only identified in one sample

We keep peptides that were observed at last twice.

pe <- filterFeatures(pe,~nNonZero >= 2)
nrow(pe[["peptideLog"]])

## [1] 17432

We keep 17432 peptides after filtering.

3.3 Normalize the data

pe <- normalize(pe, 
                i = "peptideLog", 
                name = "peptideNorm", 
                method = "center.median")

3.4 Explore normalized data

After normalisation the density curves for all samples are comparable.

limma::plotDensities(assay(pe[["peptideNorm"]]))

This is more clearly seen is a boxplot.

boxplot(assay(pe[["peptideNorm"]]), col = palette()[-1],
       main = "Peptide distribtutions after normalisation", ylab = "intensity")

We can visualize our data using a Multi Dimensional Scaling plot, eg. as provided by the limma package.

limma::plotMDS(assay(pe[["peptideNorm"]]),
  col = colData(pe)$location:colData(pe)$tissue %>%
    as.numeric,
  labels = colData(pe) %>%
    rownames %>%  
    substr(start = 11, stop = 13)
  )

The first axis in the plot is showing the leading log fold changes (differences on the log scale) between the samples.

3.5 Summarization to protein level

We use robust summarization in aggregateFeatures. This is the default workflow of aggregateFeatures so you do not have to specifiy the argument fun. However, because we compare methods we have included the fun argument to show the summarization method explicitely.

pe <- aggregateFeatures(pe,
 i = "peptideNorm",
 fcol = "Proteins",
 na.rm = TRUE,
 name = "proteinRobust",
 fun = MsCoreUtils::robustSummary)

## Your quantitative and row data contain missing values. Please read the
## relevant section(s) in the aggregateFeatures manual page regarding the
## effects of missing values on data aggregation.

plotMDS(assay(pe[["proteinRobust"]]),
  col = colData(pe)$location:colData(pe)$tissue %>%
    as.numeric,
  labels = colData(pe) %>%
    rownames %>%  
    substr(start = 11, stop = 13)
)

4 Data Analysis

4.1 Estimation

We model the protein level expression values using msqrob. By default msqrob2 estimates the model parameters using robust regression.

pe <- msqrob(
  object = pe,
  i = "proteinRobust",
  formula = ~ location*tissue + patient)

4.2 Inference

Explore Design

library(ExploreModelMatrix)
VisualizeDesign(colData(pe),~ location*tissue + patient)$plotlist

## $`location = L`

## 
## $`location = R`

design <- model.matrix(~location*tissue + patient, data = colData(pe))
L <- makeContrast(
  c(
    "tissueV = 0",
    "tissueV + locationR:tissueV = 0",
    "tissueV + 0.5*locationR:tissueV = 0","locationR:tissueV = 0"),
  parameterNames = colnames(design)
  )


pe <- hypothesisTest(object = pe, i = "proteinRobust", contrast = L, overwrite=TRUE)

4.3 Evaluate results contrast \(\log_2 FC_{V-A}^L\)

4.3.1 Volcano-plot

volcanoLeft <- ggplot(rowData(pe[["proteinRobust"]])$"tissueV",
                 aes(x = logFC, y = -log10(pval), color = adjPval < 0.05)) +
 geom_point(cex = 2.5) +
 scale_color_manual(values = alpha(c("black", "red"), 0.5)) + theme_minimal()
volcanoLeft

4.3.2 Heatmap

We first select the names of the proteins that were declared signficant.

sigNamesLeft <- rowData(pe[["proteinRobust"]])$tissueV %>%
 rownames_to_column("proteinRobust") %>%
 filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesLeft, ])

There are 199 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$tissueV %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  filter(adjPval<0.05) %>%
  arrange(pval)  %>%
  knitr::kable(.)

	logFC	se	df	t	pval	adjPval	rowData(pe[[“proteinRobust”]])$Protein.names
P08590	7.9679512	0.4374873	9.367147	18.212987	0.0000000	0.0000254	Myosin light chain 3
P12883	4.6698827	0.3716628	9.181668	12.564838	0.0000004	0.0004379	Myosin-7
P10916	6.9261087	0.5291456	7.367147	13.089231	0.0000023	0.0015506	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q6UWY5	-3.2536428	0.3828898	9.113260	-8.497596	0.0000126	0.0046705	Olfactomedin-like protein 1
O75368	-2.2715945	0.2715292	9.289260	-8.365932	0.0000127	0.0046705	SH3 domain-binding glutamic acid-rich-like protein
P46821	-2.1668803	0.2632626	9.367147	-8.230871	0.0000138	0.0046705	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
O95865	-2.1732192	0.2826203	9.367147	-7.689536	0.0000242	0.0065478	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q8N474	-3.3090235	0.3804443	7.897481	-8.697787	0.0000258	0.0065478	Secreted frizzled-related protein 1
Q9ULL5-3	-3.4165405	0.3998973	7.846127	-8.543546	0.0000305	0.0068882	Proline-rich protein 12
P14854	2.4019126	0.3057866	8.431469	7.854864	0.0000371	0.0069621	Cytochrome c oxidase subunit 6B1
P21810	-3.2145420	0.4216792	8.756796	-7.623194	0.0000378	0.0069621	Biglycan
O94875-10	2.3744000	0.3186130	8.904913	7.452301	0.0000411	0.0069621	Sorbin and SH3 domain-containing protein 2
P05546	-1.9318824	0.2699782	9.271661	-7.155698	0.0000458	0.0071533	Heparin cofactor 2
P29622	-2.1134793	0.3013433	9.367147	-7.013527	0.0000510	0.0073994	Kallistatin
Q16647	-2.7991521	0.3962438	9.028244	-7.064217	0.0000580	0.0078583	Prostacyclin synthase
P02452	-2.9630153	0.3999152	8.292268	-7.409110	0.0000627	0.0079615	Collagen alpha-1(I) chain
P51884	-2.1343314	0.3160771	9.157371	-6.752566	0.0000768	0.0091803	Lumican
Q8TBQ9	-2.8189960	0.4060648	8.622892	-6.942232	0.0000832	0.0093870	Protein kish-A
P07451	-1.8489373	0.2896256	9.367147	-6.383889	0.0001070	0.0096523	Carbonic anhydrase 3
P36955	-2.3377901	0.3356490	8.143555	-6.964984	0.0001071	0.0096523	Pigment epithelium-derived factor
P00325	-2.1119462	0.3236237	8.984001	-6.525931	0.0001090	0.0096523	Alcohol dehydrogenase 1B
Q9UBG0	-2.5547510	0.3974700	9.172396	-6.427531	0.0001115	0.0096523	C-type mannose receptor 2
P24844	-2.4962161	0.3930153	9.311934	-6.351447	0.0001143	0.0096523	Myosin regulatory light polypeptide 9
P23083	-4.2325442	0.5732249	7.367147	-7.383742	0.0001176	0.0096523	Ig heavy chain V-I region V35
P51888	-3.0081810	0.4004846	7.159338	-7.511353	0.0001214	0.0096523	Prolargin
Q15113	-2.7424988	0.4328062	9.185821	-6.336551	0.0001235	0.0096523	Procollagen C-endopeptidase enhancer 1
Q53GQ0	-2.4232423	0.3906212	9.357570	-6.203561	0.0001341	0.0098288	Very-long-chain 3-oxoacyl-CoA reductase
Q06828	-4.2030186	0.6622505	8.969004	-6.346569	0.0001354	0.0098288	Fibromodulin
P13533	-4.0404076	0.6482413	9.098373	-6.232876	0.0001458	0.0100636	Myosin-6
P35442	-2.3010500	0.3521110	8.367147	-6.535012	0.0001486	0.0100636	Thrombospondin-2
P08294	-2.7503241	0.4255134	7.961617	-6.463543	0.0001996	0.0130065	Extracellular superoxide dismutase [Cu-Zn]
Q96LL9	-2.4127080	0.3982119	8.757117	-6.058855	0.0002106	0.0130065	DnaJ homolog subfamily C member 30
P18428	-1.9996058	0.3385817	9.138659	-5.905830	0.0002142	0.0130065	Lipopolysaccharide-binding protein
P36021	-3.1085951	0.5038063	8.367147	-6.170218	0.0002229	0.0130065	Monocarboxylate transporter 8
Q9UL18	-2.6225313	0.4093678	7.860316	-6.406296	0.0002240	0.0130065	Protein argonaute-1
Q92508	4.0552373	0.5571318	6.367147	7.278776	0.0002601	0.0145405	Piezo-type mechanosensitive ion channel component 1
P46060	-1.9620904	0.3259353	8.367147	-6.019876	0.0002648	0.0145405	Ran GTPase-activating protein 1
P02743	-2.1700557	0.3848102	9.367147	-5.639288	0.0002745	0.0146795	Serum amyloid P-component;Serum amyloid P-component(1-203)
Q14764	-1.6267934	0.2898937	9.367147	-5.611689	0.0002847	0.0148124	Major vault protein
Q9UGT4	-2.3006162	0.4078630	9.191824	-5.640659	0.0002937	0.0148124	Sushi domain-containing protein 2
P05997	-3.0856148	0.5406267	8.940173	-5.707478	0.0002989	0.0148124	Collagen alpha-2(V) chain
Q8WWA0	-5.8725166	0.9875034	8.102804	-5.946832	0.0003266	0.0149420	Intelectin-1
Q9P2B2	-2.0393915	0.3730039	9.367147	-5.467480	0.0003448	0.0149420	Prostaglandin F2 receptor negative regulator
O43677	-2.7199107	0.4714089	8.430596	-5.769748	0.0003448	0.0149420	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
O60760	-3.5990151	0.6214672	8.367147	-5.791158	0.0003459	0.0149420	Hematopoietic prostaglandin D synthase
Q9UBB5	2.7451793	0.3963878	6.367147	6.925489	0.0003461	0.0149420	Methyl-CpG-binding domain protein 2
Q9BW30	-2.7245919	0.4890247	8.999217	-5.571480	0.0003468	0.0149420	Tubulin polymerization-promoting protein family member 3
P40261	-2.3445730	0.4269404	9.220700	-5.491570	0.0003530	0.0149420	Nicotinamide N-methyltransferase
P00748	-1.9914680	0.3694783	9.103103	-5.389946	0.0004220	0.0171497	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q9NZ01	-2.4109216	0.4362041	8.632777	-5.527049	0.0004254	0.0171497	Very-long-chain enoyl-CoA reductase
O14967	-2.3785961	0.4289854	8.527297	-5.544702	0.0004347	0.0171497	Calmegin
Q92736-2	-3.3064395	0.6040687	8.713491	-5.473615	0.0004404	0.0171497	Ryanodine receptor 2
P12110	-1.9881397	0.3530961	8.169020	-5.630590	0.0004568	0.0171497	Collagen alpha-2(VI) chain
Q07954	-1.6573532	0.3151479	9.367147	-5.258970	0.0004573	0.0171497	Prolow-density lipoprotein receptor-related protein 1;Low-density lipoprotein receptor-related protein 1 85 kDa subunit;Low-density lipoprotein receptor-related protein 1 515 kDa subunit;Low-density lipoprotein receptor-related protein 1 intracellular domain
O00180	-4.2526703	0.7668193	8.367147	-5.545857	0.0004642	0.0171497	Potassium channel subfamily K member 1
O95980	-2.5277905	0.4553786	8.146506	-5.550964	0.0005069	0.0183950	Reversion-inducing cysteine-rich protein with Kazal motifs
P31994-2	-1.5795166	0.3014877	9.069055	-5.239074	0.0005222	0.0186176	Low affinity immunoglobulin gamma Fc region receptor II-b
O00264	-1.9731043	0.3784495	9.044168	-5.213653	0.0005452	0.0190997	Membrane-associated progesterone receptor component 1
Q8TBP6	-1.9233155	0.3698007	8.978834	-5.200951	0.0005676	0.0193921	Solute carrier family 25 member 40
Q14195-2	-2.5380012	0.4959220	9.230176	-5.117743	0.0005819	0.0193921	Dihydropyrimidinase-related protein 3
Q8WZA9	-1.4960398	0.2916008	9.178039	-5.130437	0.0005821	0.0193921	Immunity-related GTPase family Q protein
Q9BXN1	-2.6634064	0.5179968	8.959110	-5.141743	0.0006187	0.0202775	Asporin
O43464	-1.9028432	0.3751944	9.113486	-5.071620	0.0006449	0.0207537	Serine protease HTRA2, mitochondrial
P01699	-4.3035389	0.6883928	6.248678	-6.251575	0.0006637	0.0207537	Ig lambda chain V-I region VOR
P41240	-1.5466953	0.3044926	8.997098	-5.079582	0.0006639	0.0207537	Tyrosine-protein kinase CSK
Q9GZY4	-3.1557642	0.5785316	7.722737	-5.454783	0.0006827	0.0207601	Cytochrome c oxidase assembly factor 1 homolog
P06858	1.7891922	0.3581440	9.249267	4.995735	0.0006845	0.0207601	Lipoprotein lipase
Q8NAT1	-1.3792038	0.2787226	9.307624	-4.948303	0.0007179	0.0214514	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
P04083	-1.5201990	0.3087015	9.367147	-4.924495	0.0007285	0.0214548	Annexin A1
P02747	-2.6697776	0.4696697	6.990471	-5.684373	0.0007510	0.0217991	Complement C1q subcomponent subunit C
Q92621	-1.7036447	0.3507462	9.364182	-4.857201	0.0008024	0.0226580	Nuclear pore complex protein Nup205
Q9NY15	-2.1436460	0.4431106	9.350476	-4.837723	0.0008285	0.0226580	Stabilin-1
A6NMZ7	-2.2762344	0.4709254	9.367147	-4.833535	0.0008292	0.0226580	Collagen alpha-6(VI) chain
O14980	-1.2169774	0.2518199	9.367147	-4.832729	0.0008302	0.0226580	Exportin-1
P02775	-1.9622566	0.4071167	9.367147	-4.819887	0.0008456	0.0226580	Platelet basic protein;Connective tissue-activating peptide III;TC-2;Connective tissue-activating peptide III(1-81);Beta-thromboglobulin;Neutrophil-activating peptide 2(74);Neutrophil-activating peptide 2(73);Neutrophil-activating peptide 2;TC-1;Neutrophil-activating peptide 2(1-66);Neutrophil-activating peptide 2(1-63)
Q96C86	-1.4762676	0.3026419	9.095986	-4.877936	0.0008474	0.0226580	m7GpppX diphosphatase
Q92604	-2.2504519	0.4678659	9.299173	-4.810036	0.0008754	0.0229047	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
P48681	-1.3334013	0.2781809	9.364182	-4.793288	0.0008792	0.0229047	Nestin
P50552	-1.5288544	0.3231655	8.983622	-4.730872	0.0010780	0.0267614	Vasodilator-stimulated phosphoprotein
P24311	1.7937075	0.3866324	9.367147	4.639310	0.0010976	0.0267614	Cytochrome c oxidase subunit 7B, mitochondrial
Q7L4S7	-1.7124303	0.3243476	7.099840	-5.279615	0.0010977	0.0267614	Protein ARMCX6
Q9UNW9	4.0122337	0.8559585	9.088964	4.687416	0.0011103	0.0267614	RNA-binding protein Nova-2
P49207	-1.5105253	0.3206044	8.971215	-4.711493	0.0011119	0.0267614	60S ribosomal protein L34
Q8WY22	-1.8091979	0.3730387	8.367147	-4.849894	0.0011192	0.0267614	BRI3-binding protein
P46063	-1.3496984	0.2888474	9.129952	-4.672705	0.0011201	0.0267614	ATP-dependent DNA helicase Q1
P56539	-2.0161968	0.4208374	8.545845	-4.790916	0.0011402	0.0267614	Caveolin-3
Q53GG5-2	-2.9088697	0.6016560	8.356632	-4.834772	0.0011458	0.0267614	PDZ and LIM domain protein 3
Q5M9N0	-3.5146838	0.7310929	8.332430	-4.807438	0.0011975	0.0275743	Coiled-coil domain-containing protein 158
Q6SZW1	-2.6395602	0.5186963	7.367147	-5.088836	0.0012133	0.0275743	Sterile alpha and TIR motif-containing protein 1
Q9HAV4	-2.4188578	0.4846303	7.617284	-4.991140	0.0012317	0.0275743	Exportin-5
Q5NDL2	-2.2948242	0.4878362	8.664509	-4.704088	0.0012349	0.0275743	EGF domain-specific O-linked N-acetylglucosamine transferase
Q9BXR6	-2.3571850	0.5178901	9.364182	-4.551516	0.0012492	0.0275910	Complement factor H-related protein 5
Q92681	-2.1962163	0.4494520	7.879124	-4.886432	0.0012689	0.0276210	Regulatory solute carrier protein family 1 member 1
O15230	-1.4246624	0.3043849	8.636336	-4.680464	0.0012868	0.0276210	Laminin subunit alpha-5
Q8TDB6	-1.7610737	0.3837043	9.048834	-4.589664	0.0012913	0.0276210	E3 ubiquitin-protein ligase DTX3L
Q96H79	-3.2031583	0.5750912	6.147712	-5.569827	0.0013091	0.0277092	Zinc finger CCCH-type antiviral protein 1-like
P14550	-1.3982496	0.3048344	8.802749	-4.586916	0.0013928	0.0289541	Alcohol dehydrogenase [NADP(+)]
Q15274	-1.9285076	0.4005361	7.862886	-4.814816	0.0013964	0.0289541	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q9BUF5	-1.9157084	0.4272902	9.247853	-4.483389	0.0014250	0.0292485	Tubulin beta-6 chain
O15111	-1.9484725	0.3815882	6.903146	-5.106218	0.0014499	0.0293993	Inhibitor of nuclear factor kappa-B kinase subunit alpha
Q12996	-2.0094808	0.3792349	6.440629	-5.298775	0.0014666	0.0293993	Cleavage stimulation factor subunit 3
Q9Y5U8	-4.0913780	0.9181288	9.266368	-4.456213	0.0014758	0.0293993	Mitochondrial pyruvate carrier 1
P06727	-1.3683135	0.3016512	8.787743	-4.536079	0.0015025	0.0296423	Apolipoprotein A-IV
P04196	-1.9303128	0.3967527	7.453131	-4.865279	0.0015268	0.0297383	Histidine-rich glycoprotein
O75828	-1.6544202	0.3750600	9.367147	-4.411081	0.0015367	0.0297383	Carbonyl reductase [NADPH] 3
Q9UBI9	-2.9866384	0.6065034	7.178007	-4.924355	0.0015861	0.0304047	Headcase protein homolog
P01031	-1.3157564	0.2894039	8.491718	-4.546436	0.0016166	0.0306002	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q9ULC3	-1.6333020	0.3625905	8.667470	-4.504536	0.0016264	0.0306002	Ras-related protein Rab-23
Q6ZSY5	-1.6890696	0.3854839	9.182684	-4.381686	0.0016838	0.0313439	Protein phosphatase 1 regulatory subunit 3F
P45877	-1.2442932	0.2872074	9.367147	-4.332386	0.0017287	0.0313439	Peptidyl-prolyl cis-trans isomerase C
P02461	-3.6062939	0.7973977	8.363561	-4.522579	0.0017362	0.0313439	Collagen alpha-1(III) chain
P04003	-1.5009188	0.3412304	8.969835	-4.398549	0.0017380	0.0313439	C4b-binding protein alpha chain
P14555	-4.6109150	0.9304769	6.863351	-4.955432	0.0017430	0.0313439	Phospholipase A2, membrane associated
Q8N5M1	-1.9899041	0.4556442	9.069735	-4.367233	0.0017715	0.0315764	ATP synthase mitochondrial F1 complex assembly factor 2
P08582	-1.6911943	0.3932927	9.341606	-4.300091	0.0018262	0.0322686	Melanotransferrin
Q6YN16	1.5603531	0.3639252	9.367147	4.287565	0.0018493	0.0323953	Hydroxysteroid dehydrogenase-like protein 2
P34932	-1.1578310	0.2691330	9.238541	-4.302077	0.0018681	0.0324314	Heat shock 70 kDa protein 4
Q9UQ35	-1.3570787	0.3179206	9.347887	-4.268609	0.0019120	0.0324314	Serine/arginine repetitive matrix protein 2
O75746	-1.5795706	0.3587964	8.599528	-4.402415	0.0019137	0.0324314	Calcium-binding mitochondrial carrier protein Aralar1
Q13636	-3.2633858	0.6324031	6.180434	-5.160293	0.0019152	0.0324314	Ras-related protein Rab-31
Q5VIR6-4	-1.7638024	0.4128026	9.114008	-4.272750	0.0020132	0.0332492	Vacuolar protein sorting-associated protein 53 homolog
P02776	-1.7615098	0.3921839	7.975973	-4.491540	0.0020399	0.0332492	Platelet factor 4;Platelet factor 4, short form
P04004	-1.6269790	0.3756157	8.731887	-4.331499	0.0020407	0.0332492	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
Q9H1E5	-1.3852786	0.3281323	9.367147	-4.221707	0.0020431	0.0332492	Thioredoxin-related transmembrane protein 4
P04209	1.3436120	0.3156579	9.137168	4.256545	0.0020503	0.0332492	Ig lambda chain V-II region NIG-84
P01042	-2.2103015	0.4729773	7.253167	-4.673166	0.0020736	0.0332492	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q8WWQ0	-1.6224614	0.3855331	9.367147	-4.208358	0.0020849	0.0332492	PH-interacting protein
P15924	1.2648885	0.3003716	9.330534	4.211079	0.0020944	0.0332492	Desmoplakin
Q2TAA5	-1.2916274	0.3067965	9.181244	-4.210046	0.0021742	0.0341741	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
Q9BTV4	-1.8099873	0.4311384	9.158605	-4.198158	0.0022254	0.0341741	Transmembrane protein 43
P05455	-1.2004499	0.2855126	9.117952	-4.204543	0.0022260	0.0341741	Lupus La protein
Q08945	-2.0204841	0.4657163	8.367147	-4.338444	0.0022342	0.0341741	FACT complex subunit SSRP1
Q04721	1.5358466	0.3666990	9.160307	4.188303	0.0022576	0.0341741	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
Q53T59	-1.8461756	0.4183662	7.984426	-4.412822	0.0022586	0.0341741	HCLS1-binding protein 3
Q9Y6X5	-1.3875045	0.3248443	8.651882	-4.271291	0.0022724	0.0341741	Bis(5-adenosyl)-triphosphatase ENPP4
P09619	-1.6085799	0.3850562	9.173401	-4.177519	0.0022872	0.0341741	Platelet-derived growth factor receptor beta
Q5JPH6	3.5281305	0.6835315	5.776077	5.161621	0.0023437	0.0347624	Probable glutamate–tRNA ligase, mitochondrial
O60262	-1.5577722	0.3669827	8.646805	-4.244810	0.0023634	0.0348009	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
O75348	-1.8591253	0.4525316	9.367147	-4.108278	0.0024290	0.0354146	V-type proton ATPase subunit G 1
O00303	-1.4561773	0.3498358	8.997975	-4.162459	0.0024400	0.0354146	Eukaryotic translation initiation factor 3 subunit F
P01034	-1.6978634	0.4073285	8.805921	-4.168290	0.0025357	0.0365108	Cystatin-C
P49458	-2.2735269	0.5031811	7.198623	-4.518307	0.0025514	0.0365108	Signal recognition particle 9 kDa protein
P25940	-1.7454125	0.4259273	9.102407	-4.097911	0.0026217	0.0372535	Collagen alpha-3(V) chain
P62760	-1.9146688	0.4698588	9.106554	-4.074988	0.0027113	0.0382594	Visinin-like protein 1
P08311	-1.3139510	0.3210787	8.829026	-4.092302	0.0028195	0.0395116	Cathepsin G
Q9UKS6	1.4372286	0.3534027	8.938698	4.066830	0.0028533	0.0396710	Protein kinase C and casein kinase substrate in neurons protein 3
Q14019	-3.9129083	0.8342890	6.367147	-4.690111	0.0028739	0.0396710	Coactosin-like protein
P36551	-1.3202398	0.3266579	9.025556	-4.041659	0.0029043	0.0396710	Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial
O15116	-3.2231772	0.6508255	5.741418	-4.952445	0.0029126	0.0396710	U6 snRNA-associated Sm-like protein LSm1
P30405	-1.5177122	0.3806683	9.367147	-3.986967	0.0029285	0.0396710	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q9UKX3	2.1517579	0.5372932	9.185210	4.004811	0.0029635	0.0398795	Myosin-13
Q9Y2Z0	-1.7414076	0.4387294	9.367147	-3.969206	0.0030103	0.0402423	Suppressor of G2 allele of SKP1 homolog
P54577	-1.3002728	0.3236699	8.963466	-4.017281	0.0030556	0.0405819	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
P19429	2.3063639	0.5565708	8.157979	4.143882	0.0031014	0.0409229	Troponin I, cardiac muscle
P54652	-1.5932853	0.4010215	9.078544	-3.973066	0.0031841	0.0417419	Heat shock-related 70 kDa protein 2
O75475	-1.9038879	0.4838865	9.239788	-3.934575	0.0032625	0.0424956	PC4 and SFRS1-interacting protein
P25311	-1.5051007	0.3733990	8.503030	-4.030810	0.0033366	0.0431841	Zinc-alpha-2-glycoprotein
P60468	-1.4647431	0.3603484	8.222346	-4.064796	0.0034077	0.0437568	Protein transport protein Sec61 subunit beta
Q9BS26	-1.2463986	0.3201937	9.301620	-3.892639	0.0034370	0.0437568	Endoplasmic reticulum resident protein 44
Q7LBR1	-2.8413335	0.7318250	9.367147	-3.882531	0.0034454	0.0437568	Charged multivesicular body protein 1b
Q04941	-1.9356392	0.4951845	9.068974	-3.908925	0.0035184	0.0444065	Proteolipid protein 2
P03950	-2.2030636	0.5449282	8.151933	-4.042851	0.0035784	0.0448536	Angiogenin
Q1KMD3	-1.4744120	0.3778425	9.012210	-3.902186	0.0035980	0.0448536	Heterogeneous nuclear ribonucleoprotein U-like protein 2
Q13641	-2.2297004	0.5229944	7.058658	-4.263335	0.0036607	0.0452218	Trophoblast glycoprotein
P26447	-1.8372154	0.4670885	8.705342	-3.933335	0.0036720	0.0452218	Protein S100-A4
Q96PK6	-1.3089284	0.3377403	9.065474	-3.875547	0.0037056	0.0453598	RNA-binding protein 14
Q9Y3B4	-1.2603707	0.3260635	9.015209	-3.865414	0.0038033	0.0455581	Splicing factor 3B subunit 6
Q9HB40	-2.1393191	0.4805751	6.308048	-4.451581	0.0038264	0.0455581	Retinoid-inducible serine carboxypeptidase
P01024	-1.1180307	0.2906403	9.104573	-3.846785	0.0038418	0.0455581	Complement C3;Complement C3 beta chain;C3-beta-c;Complement C3 alpha chain;C3a anaphylatoxin;Acylation stimulating protein;Complement C3b alpha chain;Complement C3c alpha chain fragment 1;Complement C3dg fragment;Complement C3g fragment;Complement C3d fragment;Complement C3f fragment;Complement C3c alpha chain fragment 2
O00567	-2.4335450	0.6370866	9.292457	-3.819803	0.0038576	0.0455581	Nucleolar protein 56
P12814	-1.6827515	0.4222152	8.156643	-3.985531	0.0038754	0.0455581	Alpha-actinin-1
Q13478	-1.6083281	0.4166997	8.944897	-3.859681	0.0038937	0.0455581	Interleukin-18 receptor 1
Q86VU5	1.5583619	0.4096879	9.367147	3.803778	0.0038984	0.0455581	Catechol O-methyltransferase domain-containing protein 1
P07384	-1.1052065	0.2894558	9.248204	-3.818222	0.0039011	0.0455581	Calpain-1 catalytic subunit
P01008	-1.5692162	0.4138323	9.323357	-3.791914	0.0040057	0.0463199	Antithrombin-III
P14543	-1.4365423	0.3761295	9.100089	-3.819276	0.0040120	0.0463199	Nidogen-1
O94919	-1.1247209	0.2951930	9.130892	-3.810121	0.0040440	0.0463461	Endonuclease domain-containing 1 protein
Q9UK22	-1.8807802	0.4297385	6.358956	-4.376569	0.0040830	0.0463461	F-box only protein 2
P07357	-1.1425305	0.3014789	9.209682	-3.789753	0.0041093	0.0463461	Complement component C8 alpha chain
Q7Z3T8	-1.6269924	0.4197584	8.532932	-3.876021	0.0041548	0.0463461	Zinc finger FYVE domain-containing protein 16
O95486	-1.7001274	0.4471105	9.024990	-3.802477	0.0041801	0.0463461	Protein transport protein Sec24A
Q9BXY0	-1.9170100	0.4360089	6.227155	-4.396722	0.0041959	0.0463461	Protein MAK16 homolog
Q14011	-2.3803571	0.6080638	8.233933	-3.914650	0.0042078	0.0463461	Cold-inducible RNA-binding protein
Q9Y2D4	-2.0300937	0.5287486	8.669332	-3.839431	0.0042572	0.0463461	Exocyst complex component 6B
Q96ST3	-1.6077298	0.4246584	9.053453	-3.785937	0.0042636	0.0463461	Paired amphipathic helix protein Sin3a
O43143	-0.9916403	0.2647264	9.367147	-3.745907	0.0042710	0.0463461	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
P56199	-1.2716373	0.3308060	8.590476	-3.844058	0.0043010	0.0463461	Integrin alpha-1
Q6IC98	-1.1710653	0.3048196	8.602633	-3.841831	0.0043038	0.0463461	GRAM domain-containing protein 4
P09467	-2.0219103	0.4940378	7.220615	-4.092623	0.0043201	0.0463461	Fructose-1,6-bisphosphatase 1
P51665	-1.2958979	0.3454369	9.244310	-3.751475	0.0043335	0.0463461	26S proteasome non-ATPase regulatory subunit 7
Q9BVC6	-1.6329609	0.4374418	9.367147	-3.732978	0.0043593	0.0463771	Transmembrane protein 109
P50991	-1.7929240	0.4656158	8.411032	-3.850651	0.0044321	0.0469059	T-complex protein 1 subunit delta
Q96FJ2	1.5408850	0.4060443	8.592028	3.794869	0.0046262	0.0487069	Dynein light chain 2, cytoplasmic
P23434	1.1390966	0.3085590	9.367147	3.691665	0.0046543	0.0487500	Glycine cleavage system H protein, mitochondrial
Q8NBF2	-1.1613746	0.3146082	9.294232	-3.691495	0.0047181	0.0491654	NHL repeat-containing protein 2
P04843	-2.0344244	0.5394883	8.618713	-3.771026	0.0047671	0.0494011	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
Q53FA7	1.8348852	0.4959980	9.147158	3.699381	0.0047894	0.0494011	Quinone oxidoreductase PIG3
Q6P1N0	-1.7290768	0.4243095	6.929225	-4.075037	0.0048218	0.0494840	Coiled-coil and C2 domain-containing protein 1A
Q6P587	5.5394450	1.3285772	6.529232	4.169457	0.0048861	0.0498918	Acylpyruvase FAHD1, mitochondrial

4.4 Evaluate results contrast \(\log_2 FC_{V-A}^R\)

4.4.1 Volcano-plot

volcanoRight <- ggplot(rowData(pe[["proteinRobust"]])$"tissueV + locationR:tissueV",
                 aes(x = logFC, y = -log10(pval), color = adjPval < 0.05)) +
 geom_point(cex = 2.5) +
 scale_color_manual(values = alpha(c("black", "red"), 0.5)) + theme_minimal()
volcanoRight

4.4.2 Heatmap

We first select the names of the proteins that were declared signficant.

sigNamesRight <- rowData(pe[["proteinRobust"]])$"tissueV + locationR:tissueV" %>%
 rownames_to_column("proteinRobust") %>%
 filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesRight, ])

There are 87 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"tissueV + locationR:tissueV"  %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)

	logFC	se	df	t	pval	adjPval	rowData(pe[[“proteinRobust”]])$Protein.names
P08590	5.503838	0.4374873	9.367147	12.580565	0.0000004	0.0007167	Myosin light chain 3
P06858	3.354674	0.3544630	9.249267	9.464102	0.0000046	0.0047205	Lipoprotein lipase
Q9ULD0	-3.575906	0.3737222	7.367147	-9.568355	0.0000205	0.0138839	2-oxoglutarate dehydrogenase-like, mitochondrial
P35442	-3.246460	0.4065828	8.367147	-7.984746	0.0000343	0.0146265	Thrombospondin-2
P02776	-2.818363	0.3421511	7.975973	-8.237189	0.0000360	0.0146265	Platelet factor 4;Platelet factor 4, short form
P21810	-2.924783	0.4081159	8.756796	-7.166550	0.0000606	0.0197128	Biglycan
O75368	-1.819326	0.2697137	9.289260	-6.745396	0.0000723	0.0197128	SH3 domain-binding glutamic acid-rich-like protein
A6NMZ7	-3.070848	0.4709254	9.367147	-6.520879	0.0000907	0.0197128	Collagen alpha-6(VI) chain
P54652	-2.726681	0.4117048	9.078544	-6.622904	0.0000929	0.0197128	Heat shock-related 70 kDa protein 2
Q6UWY5	-2.456874	0.3739352	9.113260	-6.570320	0.0000970	0.0197128	Olfactomedin-like protein 1
Q06828	-4.122091	0.6364116	8.969004	-6.477083	0.0001162	0.0198286	Fibromodulin
P05546	-1.727800	0.2722248	9.271661	-6.346960	0.0001171	0.0198286	Heparin cofactor 2
P28066	-2.176824	0.3385695	8.729782	-6.429476	0.0001385	0.0205216	Proteasome subunit alpha type-5
P29622	-1.847919	0.3013433	9.367147	-6.132273	0.0001459	0.0205216	Kallistatin
P46821	-1.606539	0.2632626	9.367147	-6.102419	0.0001515	0.0205216	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P13533	-3.888317	0.6376406	9.098373	-6.097975	0.0001718	0.0218208	Myosin-6
Q9UGT4	-2.443145	0.4143431	9.191824	-5.896430	0.0002118	0.0245753	Sushi domain-containing protein 2
P35625	-3.938312	0.6160886	7.940282	-6.392443	0.0002177	0.0245753	Metalloproteinase inhibitor 3
Q6PCB0	-2.328852	0.4033938	8.934041	-5.773148	0.0002760	0.0263652	von Willebrand factor A domain-containing protein 1
Q69YU5	3.254738	0.5557330	8.695422	5.856658	0.0002762	0.0263652	Uncharacterized protein C12orf73
Q15327	-2.203003	0.3936378	9.236415	-5.596523	0.0003057	0.0263652	Ankyrin repeat domain-containing protein 1
O43677	-2.969964	0.5063222	8.430596	-5.865758	0.0003077	0.0263652	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q14764	-1.608232	0.2898937	9.367147	-5.547661	0.0003099	0.0263652	Major vault protein
P60468	-2.438022	0.4111885	8.222346	-5.929209	0.0003148	0.0263652	Protein transport protein Sec61 subunit beta
P01031	-1.626524	0.2813193	8.491718	-5.781772	0.0003308	0.0263652	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q9P2B2	-2.035226	0.3730039	9.367147	-5.456312	0.0003500	0.0263652	Prostaglandin F2 receptor negative regulator
Q92930	-2.833666	0.4661026	7.608745	-6.079489	0.0003615	0.0263652	Ras-related protein Rab-8B
P02775	-2.205543	0.4071167	9.367147	-5.417470	0.0003688	0.0263652	Platelet basic protein;Connective tissue-activating peptide III;TC-2;Connective tissue-activating peptide III(1-81);Beta-thromboglobulin;Neutrophil-activating peptide 2(74);Neutrophil-activating peptide 2(73);Neutrophil-activating peptide 2;TC-1;Neutrophil-activating peptide 2(1-66);Neutrophil-activating peptide 2(1-63)
P48163	-2.959729	0.4884269	7.571810	-6.059718	0.0003763	0.0263652	NADP-dependent malic enzyme
P48681	-1.491288	0.2782498	9.364182	-5.359530	0.0003992	0.0269464	Nestin
P12883	1.969100	0.3654883	9.181668	5.387588	0.0004111	0.0269464	Myosin-7
P11586	2.013301	0.3518499	7.995663	5.722046	0.0004439	0.0281859	C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
P30711	-2.321740	0.4483502	9.037365	-5.178408	0.0005729	0.0337499	Glutathione S-transferase theta-1
Q9BZH6	3.442805	0.6418646	8.320379	5.363756	0.0005916	0.0337499	WD repeat-containing protein 11
Q9H1K0	-2.237374	0.3906892	7.367147	-5.726736	0.0005951	0.0337499	Rabenosyn-5
Q9UHG2	-3.175806	0.6109197	8.844100	-5.198401	0.0005979	0.0337499	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
P00748	-1.915326	0.3787289	9.103103	-5.057248	0.0006600	0.0359772	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q5NDL2	-2.708130	0.5255091	8.664509	-5.153345	0.0006772	0.0359772	EGF domain-specific O-linked N-acetylglucosamine transferase
O00180	-4.621308	0.8854466	8.367147	-5.219183	0.0006957	0.0359772	Potassium channel subfamily K member 1
Q00G26	1.964123	0.3594190	7.550595	5.464716	0.0007288	0.0359772	Perilipin-5
P23142	-2.779235	0.5081780	7.535834	-5.469018	0.0007301	0.0359772	Fibulin-1
P10916	2.921175	0.5291456	7.367147	5.520551	0.0007448	0.0359772	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q09161	2.370716	0.3866470	6.160511	6.131475	0.0007790	0.0359772	Nuclear cap-binding protein subunit 1
P18428	-1.690875	0.3454282	9.138659	-4.895012	0.0008163	0.0359772	Lipopolysaccharide-binding protein
Q9BW30	-2.326597	0.4724179	8.999217	-4.924870	0.0008193	0.0359772	Tubulin polymerization-promoting protein family member 3
P30405	-1.842938	0.3806683	9.367147	-4.841321	0.0008200	0.0359772	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q5JPH6	3.287773	0.5184763	5.776077	6.341222	0.0008350	0.0359772	Probable glutamate–tRNA ligase, mitochondrial
Q9NRG4	2.622493	0.5180883	8.367147	5.061865	0.0008499	0.0359772	N-lysine methyltransferase SMYD2
Q9BUH6	-1.485484	0.3066402	9.143080	-4.844388	0.0008750	0.0362859	Protein PAXX
P35052	-1.965366	0.3779177	7.794113	-5.200513	0.0008929	0.0362859	Glypican-1;Secreted glypican-1
O15061	-1.710970	0.3604076	9.367147	-4.747319	0.0009385	0.0373929	Synemin
P08603	-1.484314	0.3148061	9.367147	-4.715011	0.0009833	0.0384259	Complement factor H
Q96FN9	-2.712489	0.5552556	8.367147	-4.885119	0.0010687	0.0392121	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
Q8N474	-2.108536	0.4206771	7.897481	-5.012244	0.0010778	0.0392121	Secreted frizzled-related protein 1
Q04760	2.254328	0.4708264	8.729877	4.788024	0.0010784	0.0392121	Lactoylglutathione lyase
Q96KC8	-2.480944	0.5057645	8.255005	-4.905335	0.0010825	0.0392121	DnaJ homolog subfamily C member 1
P04004	-1.908509	0.3998503	8.731887	-4.773059	0.0010999	0.0392121	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
Q99983	-3.527403	0.6601201	6.896719	-5.343578	0.0011245	0.0393979	Osteomodulin
P24298	1.991397	0.4184248	8.587983	4.759271	0.0011737	0.0404238	Alanine aminotransferase 1
P62857	-2.074531	0.4153749	7.660192	-4.994359	0.0012067	0.0408654	40S ribosomal protein S28
P23434	1.406476	0.3085590	9.367147	4.558208	0.0012360	0.0411719	Glycine cleavage system H protein, mitochondrial
P24844	-1.767461	0.3911688	9.311934	-4.518410	0.0013303	0.0435996	Myosin regulatory light polypeptide 9
P04275	-1.352764	0.2984636	8.942806	-4.532424	0.0014445	0.0454140	von Willebrand factor;von Willebrand antigen 2
Q6PI78	1.975693	0.4380973	9.038962	4.509712	0.0014524	0.0454140	Transmembrane protein 65
Q15113	-1.959899	0.4399394	9.185821	-4.454929	0.0015107	0.0454140	Procollagen C-endopeptidase enhancer 1
P01611	-2.213481	0.5019811	9.367147	-4.409491	0.0015403	0.0454140	Ig kappa chain V-I region Wes
Q86WV6	-1.310297	0.2962735	9.222627	-4.422592	0.0015688	0.0454140	Stimulator of interferon genes protein
Q6UWS5	1.798858	0.3672376	7.238821	4.898350	0.0015957	0.0454140	Protein PET117 homolog, mitochondrial
P51888	-1.838614	0.3736902	7.159338	-4.920156	0.0016058	0.0454140	Prolargin
Q9BSD7	2.993219	0.6090722	7.153722	4.914392	0.0016202	0.0454140	Cancer-related nucleoside-triphosphatase
P04350	-2.861432	0.5737091	6.939826	-4.987600	0.0016280	0.0454140	Tubulin beta-4A chain
Q7L4S7	-2.514619	0.5106461	7.099840	-4.924387	0.0016369	0.0454140	Protein ARMCX6
P08294	-1.884866	0.4043438	7.961617	-4.661544	0.0016411	0.0454140	Extracellular superoxide dismutase [Cu-Zn]
P82663	-1.944516	0.4465775	9.319706	-4.354262	0.0016931	0.0454140	28S ribosomal protein S25, mitochondrial
P50453	-1.398216	0.3162925	8.945377	-4.420644	0.0016945	0.0454140	Serpin B9
P01303	-2.151374	0.4868506	8.937212	-4.418962	0.0017024	0.0454140	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
Q9UL26	7.763006	1.7509605	8.821706	4.433570	0.0017209	0.0454140	Ras-related protein Rab-22A
Q9HCB6	-2.412515	0.5438960	8.640884	-4.435619	0.0018052	0.0463162	Spondin-1
Q8TDB4	-2.849906	0.5487152	6.232826	-5.193780	0.0018053	0.0463162	Protein MGARP
Q9Y6X5	-1.531154	0.3463622	8.651882	-4.420673	0.0018379	0.0463162	Bis(5-adenosyl)-triphosphatase ENPP4
Q15274	-2.142900	0.4681074	7.862886	-4.577796	0.0018899	0.0463162	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q6YN16	1.553070	0.3639252	9.367147	4.267551	0.0019061	0.0463162	Hydroxysteroid dehydrogenase-like protein 2
P51884	-1.386041	0.3221909	9.157371	-4.301927	0.0019070	0.0463162	Lumican
P02452	-1.816507	0.4066969	8.292268	-4.466489	0.0019146	0.0463162	Collagen alpha-1(I) chain
P61925	2.031117	0.4367755	7.493224	4.650254	0.0019558	0.0467556	cAMP-dependent protein kinase inhibitor alpha
P07360	-1.535545	0.3537602	8.705608	-4.340638	0.0020285	0.0479303	Complement component C8 gamma chain
Q96MM6	3.209344	0.6626376	6.690985	4.843286	0.0021227	0.0495787	Heat shock 70 kDa protein 12B

4.5 Evaluate results average contrast \(\log_2 FC_{V-A}\)

4.5.1 Volcano-plot

volcanoAvg <- ggplot(rowData(pe[["proteinRobust"]])$"tissueV + 0.5 * locationR:tissueV",
                 aes(x = logFC, y = -log10(pval), color = adjPval < 0.05)) +
 geom_point(cex = 2.5) +
 scale_color_manual(values = alpha(c("black", "red"), 0.5)) + theme_minimal()
volcanoAvg

4.5.2 Heatmap

We first select the names of the proteins that were declared signficant.

sigNamesAvg <- rowData(pe[["proteinRobust"]])$"tissueV + 0.5 * locationR:tissueV" %>%
 rownames_to_column("proteinRobust") %>%
 filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesAvg, ])

There are 449 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"tissueV + 0.5 * locationR:tissueV" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)

	logFC	se	df	t	pval	adjPval	rowData(pe[[“proteinRobust”]])$Protein.names
P08590	6.7358945	0.3093503	9.367147	21.774329	0.0000000	0.0000049	Myosin light chain 3
P12883	3.3194914	0.2606314	9.181668	12.736345	0.0000004	0.0003891	Myosin-7
O75368	-2.0454601	0.1913593	9.289260	-10.689106	0.0000016	0.0007082	SH3 domain-binding glutamic acid-rich-like protein
Q6UWY5	-2.8552584	0.2675968	9.113260	-10.670003	0.0000019	0.0007082	Olfactomedin-like protein 1
P10916	4.9236420	0.3661150	7.367147	13.448349	0.0000019	0.0007082	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
P46821	-1.8867094	0.1861547	9.367147	-10.135167	0.0000024	0.0007082	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P06858	2.5719330	0.2519480	9.249267	10.208191	0.0000024	0.0007082	Lipoprotein lipase
P21810	-3.0696624	0.2931217	8.756796	-10.472314	0.0000030	0.0007662	Biglycan
P05546	-1.8298412	0.1916993	9.271661	-9.545370	0.0000042	0.0009134	Heparin cofactor 2
P35442	-2.7737551	0.2689292	8.367147	-10.314070	0.0000048	0.0009134	Thrombospondin-2
P29622	-1.9806994	0.2130819	9.367147	-9.295484	0.0000049	0.0009134	Kallistatin
Q06828	-4.1625547	0.4592373	8.969004	-9.064061	0.0000082	0.0013965	Fibromodulin
P13533	-3.9643622	0.4545701	9.098373	-8.721124	0.0000103	0.0016072	Myosin-6
Q8N474	-2.7087798	0.2821825	7.897481	-9.599391	0.0000126	0.0018244	Secreted frizzled-related protein 1
Q9UGT4	-2.3718806	0.2907028	9.191824	-8.159126	0.0000166	0.0020451	Sushi domain-containing protein 2
A6NMZ7	-2.6735410	0.3329946	9.367147	-8.028783	0.0000170	0.0020451	Collagen alpha-6(VI) chain
O95865	-1.5898713	0.1998428	9.367147	-7.955611	0.0000183	0.0020451	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q14764	-1.6175126	0.2049858	9.367147	-7.890852	0.0000196	0.0020451	Major vault protein
O94875-10	1.8826268	0.2305039	8.904913	8.167439	0.0000200	0.0020451	Sorbin and SH3 domain-containing protein 2
P02776	-2.2899367	0.2602286	7.975973	-8.799713	0.0000223	0.0020451	Platelet factor 4;Platelet factor 4, short form
Q9P2B2	-2.0373086	0.2637536	9.367147	-7.724288	0.0000233	0.0020451	Prostaglandin F2 receptor negative regulator
P51884	-1.7601864	0.2256721	9.157371	-7.799750	0.0000245	0.0020451	Lumican
P24844	-2.1318385	0.2772517	9.311934	-7.689181	0.0000250	0.0020451	Myosin regulatory light polypeptide 9
P02452	-2.3897612	0.2850220	8.292268	-8.384480	0.0000251	0.0020451	Collagen alpha-1(I) chain
Q16647	-2.1622988	0.2760186	9.028244	-7.833887	0.0000257	0.0020451	Prostacyclin synthase
O43677	-2.8449373	0.3457357	8.430596	-8.228647	0.0000262	0.0020451	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q15113	-2.3511987	0.3085725	9.185821	-7.619599	0.0000291	0.0021494	Procollagen C-endopeptidase enhancer 1
P18428	-1.8452405	0.2418436	9.138659	-7.629891	0.0000296	0.0021494	Lipopolysaccharide-binding protein
P54652	-2.1599833	0.2873700	9.078544	-7.516383	0.0000346	0.0024255	Heat shock-related 70 kDa protein 2
P51888	-2.4233975	0.2713558	7.159338	-8.930701	0.0000391	0.0024519	Prolargin
P00748	-1.9533971	0.2645514	9.103103	-7.383809	0.0000393	0.0024519	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
P02775	-2.0838997	0.2878750	9.367147	-7.238905	0.0000395	0.0024519	Platelet basic protein;Connective tissue-activating peptide III;TC-2;Connective tissue-activating peptide III(1-81);Beta-thromboglobulin;Neutrophil-activating peptide 2(74);Neutrophil-activating peptide 2(73);Neutrophil-activating peptide 2;TC-1;Neutrophil-activating peptide 2(1-66);Neutrophil-activating peptide 2(1-63)
Q9BW30	-2.5255943	0.3399720	8.999217	-7.428830	0.0000398	0.0024519	Tubulin polymerization-promoting protein family member 3
P48681	-1.4123446	0.1967280	9.364182	-7.179175	0.0000423	0.0025305	Nestin
P14854	1.7251878	0.2271185	8.431469	7.595980	0.0000477	0.0027296	Cytochrome c oxidase subunit 6B1
P08294	-2.3175953	0.2927458	7.961617	-7.916749	0.0000484	0.0027296	Extracellular superoxide dismutase [Cu-Zn]
O00180	-4.4369891	0.5856679	8.367147	-7.575947	0.0000507	0.0027866	Potassium channel subfamily K member 1
P02743	-1.8823835	0.2721019	9.367147	-6.917936	0.0000569	0.0030416	Serum amyloid P-component;Serum amyloid P-component(1-203)
P01031	-1.4711401	0.2020638	8.491718	-7.280573	0.0000630	0.0032847	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q5NDL2	-2.5014769	0.3585192	8.664509	-6.977247	0.0000782	0.0039740	EGF domain-specific O-linked N-acetylglucosamine transferase
Q92508	3.5430878	0.3987270	6.367147	8.885999	0.0000808	0.0040040	Piezo-type mechanosensitive ion channel component 1
Q53GQ0	-1.8169289	0.2763216	9.357570	-6.575413	0.0000854	0.0040212	Very-long-chain 3-oxoacyl-CoA reductase
P05997	-2.5486728	0.3783581	8.940173	-6.736140	0.0000877	0.0040212	Collagen alpha-2(V) chain
P60468	-1.9513827	0.2743815	8.222346	-7.111933	0.0000880	0.0040212	Protein transport protein Sec61 subunit beta
P23083	-3.2601200	0.4233546	7.367147	-7.700684	0.0000891	0.0040212	Ig heavy chain V-I region V35
Q9ULL5-3	-2.3006667	0.3151296	7.846127	-7.300700	0.0000925	0.0040854	Proline-rich protein 12
Q8TBP6	-1.7084465	0.2569535	8.978834	-6.648854	0.0000949	0.0041019	Solute carrier family 25 member 40
P28066	-1.6712466	0.2476893	8.729782	-6.747351	0.0000969	0.0041019	Proteasome subunit alpha type-5
P35625	-2.9679404	0.4157016	7.940282	-7.139594	0.0001018	0.0042130	Metalloproteinase inhibitor 3
Q14195-2	-2.2534620	0.3485664	9.230176	-6.464943	0.0001037	0.0042130	Dihydropyrimidinase-related protein 3
P46060	-1.7047689	0.2489372	8.367147	-6.848188	0.0001062	0.0042314	Ran GTPase-activating protein 1
Q15327	-1.7740861	0.2767541	9.236415	-6.410333	0.0001103	0.0043112	Ankyrin repeat domain-containing protein 1
Q9ULD0	-2.0406330	0.2760121	7.367147	-7.393273	0.0001166	0.0043340	2-oxoglutarate dehydrogenase-like, mitochondrial
Q6PCB0	-1.8163629	0.2803666	8.934041	-6.478527	0.0001181	0.0043340	von Willebrand factor A domain-containing protein 1
P00325	-1.5034066	0.2330514	8.984001	-6.450965	0.0001189	0.0043340	Alcohol dehydrogenase 1B
Q69YU5	2.5059630	0.3814793	8.695422	6.569066	0.0001203	0.0043340	Uncharacterized protein C12orf73
P07451	-1.2833190	0.2047962	9.367147	-6.266322	0.0001236	0.0043340	Carbonic anhydrase 3
O14980	-1.1146843	0.1780636	9.367147	-6.260035	0.0001245	0.0043340	Exportin-1
P30405	-1.6803249	0.2691732	9.367147	-6.242542	0.0001273	0.0043340	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q92604	-2.0782169	0.3317997	9.299173	-6.263469	0.0001280	0.0043340	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
P04004	-1.7677440	0.2743025	8.731887	-6.444506	0.0001360	0.0045115	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P36955	-1.6933164	0.2522805	8.143555	-6.712038	0.0001390	0.0045115	Pigment epithelium-derived factor
P41240	-1.3344948	0.2115614	8.997098	-6.307837	0.0001399	0.0045115	Tyrosine-protein kinase CSK
P04083	-1.3421955	0.2182849	9.367147	-6.148823	0.0001430	0.0045388	Annexin A1
P36021	-2.5034435	0.3847884	8.367147	-6.506026	0.0001534	0.0047941	Monocarboxylate transporter 8
Q6YN16	1.5567113	0.2573340	9.367147	6.049381	0.0001619	0.0049854	Hydroxysteroid dehydrogenase-like protein 2
Q8TBQ9	-1.7482778	0.2776959	8.622892	-6.295657	0.0001703	0.0051640	Protein kish-A
Q15274	-2.0357040	0.3068983	7.862886	-6.633155	0.0001768	0.0052039	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q8WWA0	-4.4529908	0.6849394	8.102804	-6.501292	0.0001776	0.0052039	Intelectin-1
Q9BXN1	-2.2858485	0.3737852	8.959110	-6.115406	0.0001793	0.0052039	Asporin
P04003	-1.4359842	0.2367633	8.969835	-6.065061	0.0001896	0.0054263	C4b-binding protein alpha chain
O15230	-1.3744676	0.2231459	8.636336	-6.159502	0.0001980	0.0055021	Laminin subunit alpha-5
Q9Y6X5	-1.4593292	0.2374292	8.651882	-6.146375	0.0001996	0.0055021	Bis(5-adenosyl)-triphosphatase ENPP4
Q7L4S7	-2.1135247	0.3024735	7.099840	-6.987472	0.0002004	0.0055021	Protein ARMCX6
P14550	-1.3048277	0.2159043	8.802749	-6.043546	0.0002100	0.0056906	Alcohol dehydrogenase [NADP(+)]
P23434	1.2727864	0.2181842	9.367147	5.833541	0.0002132	0.0056998	Glycine cleavage system H protein, mitochondrial
Q07954	-1.2959588	0.2228432	9.367147	-5.815564	0.0002182	0.0057577	Prolow-density lipoprotein receptor-related protein 1;Low-density lipoprotein receptor-related protein 1 85 kDa subunit;Low-density lipoprotein receptor-related protein 1 515 kDa subunit;Low-density lipoprotein receptor-related protein 1 intracellular domain
Q9UBG0	-1.6345146	0.2786041	9.172396	-5.866800	0.0002217	0.0057705	C-type mannose receptor 2
P49207	-1.3710319	0.2313176	8.971215	-5.927053	0.0002243	0.0057705	60S ribosomal protein L34
Q9BUF5	-1.7682813	0.3037327	9.247853	-5.821834	0.0002274	0.0057761	Tubulin beta-6 chain
P23142	-2.2973847	0.3519977	7.535834	-6.526703	0.0002375	0.0059567	Fibulin-1
P04196	-1.6877176	0.2571664	7.453131	-6.562746	0.0002404	0.0059567	Histidine-rich glycoprotein
Q9NRG4	2.3970480	0.3956965	8.367147	6.057794	0.0002535	0.0062051	N-lysine methyltransferase SMYD2
Q9NZ01	-1.8635396	0.3140785	8.632777	-5.933357	0.0002590	0.0062235	Very-long-chain enoyl-CoA reductase
O95980	-1.9294212	0.3147734	8.146506	-6.129555	0.0002603	0.0062235	Reversion-inducing cysteine-rich protein with Kazal motifs
P04275	-1.1968998	0.2066544	8.942806	-5.791793	0.0002686	0.0063466	von Willebrand factor;von Willebrand antigen 2
P12110	-1.5935296	0.2627194	8.169020	-6.065519	0.0002766	0.0064602	Collagen alpha-2(VI) chain
O75828	-1.4912698	0.2652075	9.367147	-5.623030	0.0002805	0.0064760	Carbonyl reductase [NADPH] 3
P07357	-1.1909118	0.2117180	9.209682	-5.624991	0.0002976	0.0067011	Complement component C8 alpha chain
Q9BZH6	2.6654497	0.4489571	8.320379	5.936981	0.0002979	0.0067011	WD repeat-containing protein 11
Q5JPH6	3.4079519	0.4420923	5.776077	7.708689	0.0003001	0.0067011	Probable glutamate–tRNA ligase, mitochondrial
Q86WV6	-1.1787564	0.2108524	9.222627	-5.590434	0.0003098	0.0068418	Stimulator of interferon genes protein
P24298	1.6449487	0.2841426	8.587983	5.789167	0.0003142	0.0068657	Alanine aminotransferase 1
P62760	-1.8748180	0.3363627	9.106554	-5.573799	0.0003314	0.0071510	Visinin-like protein 1
P01024	-1.1291448	0.2030347	9.104573	-5.561340	0.0003370	0.0071510	Complement C3;Complement C3 beta chain;C3-beta-c;Complement C3 alpha chain;C3a anaphylatoxin;Acylation stimulating protein;Complement C3b alpha chain;Complement C3c alpha chain fragment 1;Complement C3dg fragment;Complement C3g fragment;Complement C3d fragment;Complement C3f fragment;Complement C3c alpha chain fragment 2
P30711	-1.7974916	0.3221275	9.037365	-5.580063	0.0003378	0.0071510	Glutathione S-transferase theta-1
Q9UHG2	-2.3658698	0.4208616	8.844100	-5.621492	0.0003466	0.0072310	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
Q92681	-1.8052155	0.3015876	7.879124	-5.985708	0.0003487	0.0072310	Regulatory solute carrier protein family 1 member 1
Q9UQ35	-1.2247564	0.2246222	9.347887	-5.452518	0.0003543	0.0072728	Serine/arginine repetitive matrix protein 2
Q9HCB6	-2.0954145	0.3704574	8.640884	-5.656290	0.0003612	0.0073089	Spondin-1
P12814	-1.9016090	0.3261513	8.156643	-5.830451	0.0003637	0.0073089	Alpha-actinin-1
P48163	-1.9351889	0.3180966	7.571810	-6.083652	0.0003669	0.0073089	NADP-dependent malic enzyme
Q9Y3B4	-1.2875533	0.2342226	9.015209	-5.497136	0.0003793	0.0073286	Splicing factor 3B subunit 6
P25940	-1.6429098	0.3007525	9.102407	-5.462664	0.0003836	0.0073286	Collagen alpha-3(V) chain
P50453	-1.2078225	0.2193000	8.945377	-5.507626	0.0003846	0.0073286	Serpin B9
Q53GG5-2	-2.4399434	0.4282784	8.356632	-5.697097	0.0003886	0.0073286	PDZ and LIM domain protein 3
Q5M9N0	-2.7584485	0.4839666	8.332430	-5.699667	0.0003916	0.0073286	Coiled-coil domain-containing protein 158
P07585	-2.1323372	0.3937116	9.206541	-5.415987	0.0003922	0.0073286	Decorin
P49458	-1.8786710	0.3023835	7.198623	-6.212876	0.0003931	0.0073286	Signal recognition particle 9 kDa protein
P19429	2.2365865	0.3890238	8.157979	5.749227	0.0003994	0.0073776	Troponin I, cardiac muscle
Q53T59	-1.8080103	0.3112094	7.984426	-5.809627	0.0004037	0.0073900	HCLS1-binding protein 3
Q9UNW9	3.3060326	0.6124605	9.088964	5.397953	0.0004198	0.0076164	RNA-binding protein Nova-2
O94919	-1.1297756	0.2100645	9.130892	-5.378231	0.0004242	0.0076276	Endonuclease domain-containing 1 protein
P02747	-1.8530999	0.2972462	6.990471	-6.234226	0.0004330	0.0077188	Complement C1q subcomponent subunit C
P01008	-1.5453986	0.2920813	9.323357	-5.290988	0.0004446	0.0078553	Antithrombin-III
Q00G26	1.4810539	0.2508346	7.550595	5.904504	0.0004488	0.0078619	Perilipin-5
O00264	-1.4077482	0.2635376	9.044168	-5.341736	0.0004598	0.0079851	Membrane-associated progesterone receptor component 1
O60760	-2.2693850	0.4110619	8.367147	-5.520786	0.0004786	0.0082004	Hematopoietic prostaglandin D synthase
Q6SZW1	-2.0732831	0.3497050	7.367147	-5.928664	0.0004802	0.0082004	Sterile alpha and TIR motif-containing protein 1
Q9ULC3	-1.4313739	0.2659109	8.667470	-5.382908	0.0005032	0.0085209	Ras-related protein Rab-23
Q9BS26	-1.1794250	0.2270494	9.301620	-5.194575	0.0005110	0.0085811	Endoplasmic reticulum resident protein 44
Q8WZA9	-1.0848657	0.2079795	9.178039	-5.216213	0.0005181	0.0086196	Immunity-related GTPase family Q protein
P14543	-1.3732462	0.2626950	9.100089	-5.227532	0.0005245	0.0086196	Nidogen-1
P08603	-1.1479994	0.2226015	9.367147	-5.157195	0.0005260	0.0086196	Complement factor H
Q9BTV4	-1.5944595	0.3065542	9.158605	-5.201232	0.0005323	0.0086531	Transmembrane protein 43
Q2TAA5	-1.1153927	0.2187826	9.181244	-5.098178	0.0006078	0.0097837	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
P11586	1.2736427	0.2337934	7.995663	5.447726	0.0006115	0.0097837	C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
Q9UKR5	-3.6937409	0.7006736	8.494780	-5.271700	0.0006198	0.0098388	Probable ergosterol biosynthetic protein 28
Q9UJC5	-1.2143605	0.2412176	9.327075	-5.034295	0.0006324	0.0098644	SH3 domain-binding glutamic acid-rich-like protein 2
Q8WY22	-1.5074312	0.2849130	8.367147	-5.290848	0.0006358	0.0098644	BRI3-binding protein
P13671	-1.3576211	0.2703926	9.367147	-5.020926	0.0006359	0.0098644	Complement component C6
O14967	-1.6233066	0.3123358	8.527297	-5.197312	0.0006731	0.0103125	Calmegin
Q6PI78	1.5422623	0.3049881	9.038962	5.056795	0.0006750	0.0103125	Transmembrane protein 65
P01042	-1.9829048	0.3517972	7.253167	-5.636499	0.0006932	0.0105123	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q8WWQ0	-1.3446280	0.2726131	9.367147	-4.932367	0.0007205	0.0108231	PH-interacting protein
Q92621	-1.2226648	0.2480457	9.364182	-4.929192	0.0007244	0.0108231	Nuclear pore complex protein Nup205
Q12996	-1.6262833	0.2703269	6.440629	-6.015988	0.0007314	0.0108483	Cleavage stimulation factor subunit 3
Q9HAT2	1.5992357	0.3232890	9.218017	4.946769	0.0007404	0.0108638	Sialate O-acetylesterase
P20774	-1.9551933	0.3704602	8.016847	-5.277741	0.0007431	0.0108638	Mimecan
Q9BUH6	-1.0828646	0.2190953	9.143080	-4.942437	0.0007631	0.0110517	Protein PAXX
Q16082	-1.2629563	0.2540453	9.006163	-4.971383	0.0007669	0.0110517	Heat shock protein beta-2
Q8TDB4	-2.3381087	0.3845752	6.232826	-6.079718	0.0007805	0.0111689	Protein MGARP
P45877	-0.9878277	0.2030863	9.367147	-4.864079	0.0007938	0.0112803	Peptidyl-prolyl cis-trans isomerase C
Q14314	-1.9054905	0.3928604	9.364182	-4.850299	0.0008103	0.0113714	Fibroleukin
P35052	-1.2972987	0.2457864	7.794113	-5.278154	0.0008140	0.0113714	Glypican-1;Secreted glypican-1
P02461	-2.9334098	0.5758974	8.363561	-5.093632	0.0008170	0.0113714	Collagen alpha-1(III) chain
P02790	-1.3146905	0.2719937	9.353505	-4.833533	0.0008327	0.0115102	Hemopexin
P01034	-1.4676678	0.2965091	8.805921	-4.949824	0.0008443	0.0115926	Cystatin-C
Q86VP6	-1.3506010	0.2705069	8.499745	-4.992852	0.0008861	0.0119837	Cullin-associated NEDD8-dissociated protein 1
P40261	-1.4439118	0.2999879	9.220700	-4.813234	0.0008926	0.0119837	Nicotinamide N-methyltransferase
Q86VU5	1.3843626	0.2896931	9.367147	4.778721	0.0008970	0.0119837	Catechol O-methyltransferase domain-containing protein 1
P50479	-2.0822296	0.4095162	8.138814	-5.084608	0.0008989	0.0119837	PDZ and LIM domain protein 4
P28300	-1.4644405	0.2816641	7.771987	-5.199244	0.0009023	0.0119837	Protein-lysine 6-oxidase
P06727	-1.0726685	0.2190586	8.787743	-4.896720	0.0009128	0.0120437	Apolipoprotein A-IV
Q15126	-0.9960340	0.2092383	9.367147	-4.760285	0.0009211	0.0120757	Phosphomevalonate kinase
O95183	-1.4512639	0.3056637	9.367147	-4.747910	0.0009377	0.0121489	Vesicle-associated membrane protein 5
Q9HAV4	-1.8358132	0.3517013	7.617284	-5.219807	0.0009387	0.0121489	Exportin-5
Q9NRX4	1.4050508	0.2946648	9.218297	4.768303	0.0009521	0.0122446	14 kDa phosphohistidine phosphatase
Q96H79	-2.2370397	0.3813014	6.147712	-5.866853	0.0009945	0.0127098	Zinc finger CCCH-type antiviral protein 1-like
O43175	-2.0597036	0.4347016	9.168272	-4.738201	0.0010088	0.0127643	D-3-phosphoglycerate dehydrogenase
O43143	-0.8789725	0.1871898	9.367147	-4.695622	0.0010113	0.0127643	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
P13667	-1.0953363	0.2314854	9.119006	-4.731772	0.0010333	0.0129605	Protein disulfide-isomerase A4
P34932	-0.8861862	0.1892373	9.238541	-4.682936	0.0010693	0.0133298	Heat shock 70 kDa protein 4
Q15582	-2.2645249	0.4552426	8.014872	-4.974325	0.0010812	0.0133966	Transforming growth factor-beta-induced protein ig-h3
Q09161	1.9700086	0.3420113	6.160511	5.760068	0.0010885	0.0134056	Nuclear cap-binding protein subunit 1
Q9NY15	-1.4385610	0.3131075	9.350476	-4.594463	0.0011774	0.0143455	Stabilin-1
Q9UKX3	1.7720370	0.3830789	9.185210	4.625776	0.0011790	0.0143455	Myosin-13
P46940	-1.1105871	0.2405449	9.186608	-4.616963	0.0011936	0.0144365	Ras GTPase-activating-like protein IQGAP1
P00747	-0.8238672	0.1804762	9.352906	-4.564962	0.0012286	0.0147719	Plasminogen;Plasmin heavy chain A;Activation peptide;Angiostatin;Plasmin heavy chain A, short form;Plasmin light chain B
P26447	-1.4990741	0.3198728	8.705342	-4.686469	0.0012491	0.0149306	Protein S100-A4
O60262	-1.2559109	0.2675541	8.646805	-4.694045	0.0012589	0.0149600	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
Q96CS3	-1.1510089	0.2499452	9.038275	-4.605044	0.0012671	0.0149699	FAS-associated factor 2
Q6UWS5	1.3529266	0.2661807	7.238821	5.082738	0.0012889	0.0151393	Protein PET117 homolog, mitochondrial
P01019	-1.0239723	0.2237842	9.074108	-4.575714	0.0013079	0.0152738	Angiotensinogen;Angiotensin-1;Angiotensin-2;Angiotensin-3;Angiotensin-4;Angiotensin 1-9;Angiotensin 1-7;Angiotensin 1-5;Angiotensin 1-4
O95445	-2.5298428	0.5528311	9.048550	-4.576159	0.0013166	0.0152881	Apolipoprotein M
P27658	-1.6133702	0.3584675	9.367147	-4.500743	0.0013452	0.0154957	Collagen alpha-1(VIII) chain;Vastatin
Q96JB2	-2.0512914	0.4356596	8.367147	-4.708473	0.0013498	0.0154957	Conserved oligomeric Golgi complex subunit 3
Q07507	-1.2545210	0.2597679	7.875411	-4.829391	0.0013649	0.0155430	Dermatopontin
Q9BXV9	1.4430515	0.3197650	9.236097	4.512850	0.0013692	0.0155430	Uncharacterized protein C14orf142
P09619	-1.2391198	0.2746989	9.173401	-4.510829	0.0013970	0.0157710	Platelet-derived growth factor receptor beta
P02748	-1.2229145	0.2680492	8.859765	-4.562276	0.0014181	0.0159198	Complement component C9;Complement component C9a;Complement component C9b
Q96LL9	-1.2440322	0.2732560	8.757117	-4.552625	0.0014812	0.0165370	DnaJ homolog subfamily C member 30
Q04721	1.1483233	0.2577610	9.160307	4.454993	0.0015210	0.0168887	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
Q92930	-1.4774889	0.3068236	7.608745	-4.815434	0.0015302	0.0168985	Ras-related protein Rab-8B
Q9UQR1	-1.7724910	0.3594710	7.180587	-4.930831	0.0015726	0.0172148	Zinc finger protein 148
P54577	-1.0184999	0.2281956	8.963466	-4.463276	0.0015857	0.0172148	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
O95486	-1.3819063	0.3110258	9.024990	-4.443060	0.0016054	0.0172148	Protein transport protein Sec24A
Q99983	-2.9528995	0.5887443	6.896719	-5.015589	0.0016072	0.0172148	Osteomodulin
P83916	-1.6056296	0.3062141	6.367147	-5.243487	0.0016080	0.0172148	Chromobox protein homolog 1
P03950	-1.7791248	0.3843910	8.151933	-4.628425	0.0016096	0.0172148	Angiogenin
Q9UBV8	-1.1380629	0.2554518	8.904086	-4.455098	0.0016310	0.0173521	Peflin
P15924	0.9266546	0.2127246	9.330534	4.356123	0.0016837	0.0177527	Desmoplakin
Q7Z3T8	-1.3746348	0.3051479	8.532932	-4.504815	0.0016911	0.0177527	Zinc finger FYVE domain-containing protein 16
P00352	-1.1346512	0.2480636	8.198138	-4.574033	0.0017049	0.0177527	Retinal dehydrogenase 1
Q9H1E5	-1.0067111	0.2320246	9.367147	-4.338812	0.0017121	0.0177527	Thioredoxin-related transmembrane protein 4
O75489	1.0163873	0.2344989	9.367147	4.334294	0.0017238	0.0177527	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
O15061	-1.1041834	0.2548466	9.367147	-4.332737	0.0017278	0.0177527	Synemin
P62857	-1.3551185	0.2882275	7.660192	-4.701559	0.0017298	0.0177527	40S ribosomal protein S28
P80723	-1.5107829	0.3279264	7.974199	-4.607079	0.0017540	0.0178587	Brain acid soluble protein 1
Q9NS69	-1.0847694	0.2446335	8.742188	-4.434265	0.0017577	0.0178587	Mitochondrial import receptor subunit TOM22 homolog
P19447	-1.5879548	0.3333631	7.367147	-4.763439	0.0017829	0.0180246	TFIIH basal transcription factor complex helicase XPB subunit
Q96CX2	-0.9045513	0.2093907	9.288020	-4.319920	0.0017965	0.0180720	BTB/POZ domain-containing protein KCTD12
Q9NS86	-0.9960486	0.2292336	9.071255	-4.345126	0.0018291	0.0183094	LanC-like protein 2
P52907	-0.8523732	0.1989963	9.367147	-4.283362	0.0018611	0.0185363	F-actin-capping protein subunit alpha-1
Q08945	-1.3761500	0.3080424	8.367147	-4.467405	0.0018701	0.0185363	FACT complex subunit SSRP1
Q9BYN0	-1.2801043	0.2972007	9.118184	-4.307206	0.0019110	0.0187263	Sulfiredoxin-1
O15118	-2.1247916	0.4187294	6.367147	-5.074379	0.0019118	0.0187263	Niemann-Pick C1 protein
Q9UBB5	1.4388020	0.2836861	6.367147	5.071810	0.0019169	0.0187263	Methyl-CpG-binding domain protein 2
P62328	-1.3455146	0.2882652	7.466159	-4.667628	0.0019328	0.0187340	Thymosin beta-4;Hematopoietic system regulatory peptide
Q9Y287	-1.6105936	0.3774310	9.304864	-4.267253	0.0019361	0.0187340	Integral membrane protein 2B;BRI2, membrane form;BRI2 intracellular domain;BRI2C, soluble form;Bri23 peptide
Q8N142	1.0768090	0.2519194	9.226437	4.274419	0.0019527	0.0188053	Adenylosuccinate synthetase isozyme 1
Q14118	-0.8487363	0.1948039	8.728528	-4.356875	0.0019698	0.0188802	Dystroglycan;Alpha-dystroglycan;Beta-dystroglycan
P82663	-1.3399129	0.3163369	9.319706	-4.235714	0.0020231	0.0192998	28S ribosomal protein S25, mitochondrial
P31323	-0.9232942	0.2175171	9.195650	-4.244697	0.0020570	0.0194421	cAMP-dependent protein kinase type II-beta regulatory subunit
Q8NAT1	-0.8308927	0.1965873	9.307624	-4.226584	0.0020571	0.0194421	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
P61009	-0.8882212	0.2042775	8.542190	-4.348111	0.0020990	0.0196584	Signal peptidase complex subunit 3
Q07065	-0.9488623	0.2216917	8.906519	-4.280098	0.0020993	0.0196584	Cytoskeleton-associated protein 4
P50991	-1.5101244	0.3455712	8.411032	-4.369937	0.0021122	0.0196878	T-complex protein 1 subunit delta
P07384	-0.8641607	0.2057518	9.248204	-4.200015	0.0021720	0.0201526	Calpain-1 catalytic subunit
Q6IC98	-0.9057366	0.2102891	8.602633	-4.307102	0.0021879	0.0202081	GRAM domain-containing protein 4
A5D6W6	-2.1994339	0.4938622	7.795927	-4.453538	0.0022695	0.0207742	Fat storage-inducing transmembrane protein 1
P05455	-0.8562036	0.2042684	9.117952	-4.191561	0.0022696	0.0207742	Lupus La protein
Q96AG4	-1.0641384	0.2559798	9.296639	-4.157119	0.0022913	0.0208786	Leucine-rich repeat-containing protein 59
Q12988	-1.0103210	0.2428865	9.202381	-4.159643	0.0023335	0.0211686	Heat shock protein beta-3
Q04760	1.3958984	0.3310679	8.729877	4.216351	0.0024100	0.0217654	Lactoylglutathione lyase
P13796	-0.8819572	0.2124198	9.076454	-4.151955	0.0024322	0.0217898	Plastin-2
Q8IYI6	-0.9330152	0.2270946	9.356285	-4.108487	0.0024342	0.0217898	Exocyst complex component 8
P62277	-1.3005300	0.3165707	9.327670	-4.108183	0.0024512	0.0218455	40S ribosomal protein S13
P61925	1.3913131	0.3116727	7.493224	4.464020	0.0024694	0.0218598	cAMP-dependent protein kinase inhibitor alpha
P50238	-1.7621993	0.4213461	8.807847	-4.182309	0.0024830	0.0218598	Cysteine-rich protein 1
Q9H1K0	-1.6022771	0.3566488	7.367147	-4.492591	0.0024850	0.0218598	Rabenosyn-5
Q96A65	-0.8321129	0.2036068	9.364182	-4.086862	0.0025118	0.0220002	Exocyst complex component 4
P05543	-1.1801143	0.2627016	7.295488	-4.492224	0.0025477	0.0222182	Thyroxine-binding globulin
Q9UK22	-1.3974278	0.2914738	6.358956	-4.794352	0.0025769	0.0223772	F-box only protein 2
Q9Y490	-0.8597753	0.2099433	9.135353	-4.095275	0.0026121	0.0225867	Talin-1
P62745	-1.1929691	0.2867921	8.676677	-4.159700	0.0026518	0.0228325	Rho-related GTP-binding protein RhoB
P24311	1.1056319	0.2733904	9.367147	4.044151	0.0026807	0.0229840	Cytochrome c oxidase subunit 7B, mitochondrial
O00625	-1.1028338	0.2729181	9.367147	-4.040897	0.0026942	0.0230026	Pirin
P58546	-1.2963604	0.3154608	8.895643	-4.109419	0.0027055	0.0230028	Myotrophin
O75348	-1.2891767	0.3199881	9.367147	-4.028827	0.0027449	0.0232122	V-type proton ATPase subunit G 1
Q96FN9	-1.7766077	0.4240835	8.367147	-4.189288	0.0027530	0.0232122	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
P04843	-1.5241453	0.3687846	8.618713	-4.132887	0.0027972	0.0234873	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
P63316	0.8794535	0.2197789	9.367147	4.001537	0.0028631	0.0236255	Troponin C, slow skeletal and cardiac muscles
Q9UL18	-1.3184619	0.3093938	7.860316	-4.261436	0.0028692	0.0236255	Protein argonaute-1
Q9HB40	-1.4736038	0.3126602	6.308048	-4.713116	0.0028735	0.0236255	Retinoid-inducible serine carboxypeptidase
Q9Y4W6	0.9189304	0.2288400	9.243362	4.015602	0.0028780	0.0236255	AFG3-like protein 2
Q96C86	-0.8529077	0.2113253	9.095986	-4.035995	0.0028829	0.0236255	m7GpppX diphosphatase
Q8N5M1	-1.2833584	0.3177262	9.069735	-4.039196	0.0028860	0.0236255	ATP synthase mitochondrial F1 complex assembly factor 2
Q96GK7	-1.2557512	0.2950941	7.857234	-4.255426	0.0028951	0.0236255	Fumarylacetoacetate hydrolase domain-containing protein 2A
Q6P1N0	-1.6508051	0.3683205	6.929225	-4.481980	0.0029325	0.0237727	Coiled-coil and C2 domain-containing protein 1A
Q3ZCW2	-1.3933792	0.3090503	6.830204	-4.508585	0.0029454	0.0237727	Galectin-related protein
Q9NQZ5	1.3550021	0.3369992	9.098828	4.020788	0.0029482	0.0237727	StAR-related lipid transfer protein 7, mitochondrial
Q9UKS6	0.9882506	0.2447019	8.938698	4.038590	0.0029763	0.0238227	Protein kinase C and casein kinase substrate in neurons protein 3
P00492	-0.9642312	0.2388739	8.949664	-4.036570	0.0029778	0.0238227	Hypoxanthine-guanine phosphoribosyltransferase
Q15125	-1.5522594	0.3853057	8.978077	-4.028644	0.0029939	0.0238576	3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Q9NNX1	3.4412993	0.7419277	6.367147	4.638321	0.0030410	0.0240461	Tuftelin
Q00577	-1.0249972	0.2547649	8.944439	-4.023306	0.0030413	0.0240461	Transcriptional activator protein Pur-alpha
Q53FA7	1.3758827	0.3472370	9.147158	3.962374	0.0031885	0.0251121	Quinone oxidoreductase PIG3
P14555	-3.1616763	0.7155425	6.863351	-4.418573	0.0032377	0.0253900	Phospholipase A2, membrane associated
Q9UHD9	-0.8978150	0.2263883	9.027970	-3.965820	0.0032552	0.0253900	Ubiquilin-2
P25311	-1.0782056	0.2665328	8.503030	-4.045301	0.0032673	0.0253900	Zinc-alpha-2-glycoprotein
O95810	-0.7267426	0.1854365	9.338276	-3.919091	0.0032737	0.0253900	Serum deprivation-response protein
P09467	-1.4304382	0.3321043	7.220615	-4.307195	0.0032890	0.0253990	Fructose-1,6-bisphosphatase 1
P50552	-0.9233883	0.2329868	8.983622	-3.963265	0.0032999	0.0253990	Vasodilator-stimulated phosphoprotein
P53618	-0.9076351	0.2333972	9.367147	-3.888800	0.0034118	0.0260727	Coatomer subunit beta
P01303	-1.3886725	0.3517668	8.937212	-3.947708	0.0034131	0.0260727	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
Q7L4E1	-1.9056994	0.4891659	9.150716	-3.895814	0.0035286	0.0266991	Protein FAM73B
O15031	-0.9094327	0.2322841	9.005474	-3.915175	0.0035327	0.0266991	Plexin-B2
Q9BVC6	-1.1958920	0.3093181	9.367147	-3.866221	0.0035345	0.0266991	Transmembrane protein 109
Q92575	-0.9922287	0.2514071	8.702687	-3.946701	0.0036021	0.0269592	UBX domain-containing protein 4
P28070	-0.9263111	0.2265077	7.878722	-4.089535	0.0036028	0.0269592	Proteasome subunit beta type-4
Q8IYU8	-3.0629900	0.6834863	6.367147	-4.481421	0.0036175	0.0269592	Calcium uptake protein 2, mitochondrial
Q96MM6	1.8061841	0.4127960	6.690985	4.375488	0.0036220	0.0269592	Heat shock 70 kDa protein 12B
Q7KZF4	-0.8794696	0.2290348	9.367147	-3.839895	0.0036834	0.0272425	Staphylococcal nuclease domain-containing protein 1
P21980	-0.9178411	0.2354278	8.923692	-3.898610	0.0036868	0.0272425	Protein-glutamine gamma-glutamyltransferase 2
Q14258	-0.9919848	0.2474855	8.198155	-4.008255	0.0037141	0.0273442	E3 ubiquitin/ISG15 ligase TRIM25
A6NDG6	1.0711621	0.2778742	9.117839	3.854845	0.0037841	0.0275447	Phosphoglycolate phosphatase
Q8IUX7	-2.3978246	0.4997562	5.504662	-4.797989	0.0037921	0.0275447	Adipocyte enhancer-binding protein 1
P43121	-1.0780079	0.2729178	8.458685	-3.949937	0.0037923	0.0275447	Cell surface glycoprotein MUC18
P14625	-0.9671286	0.2529807	9.349955	-3.822935	0.0037955	0.0275447	Endoplasmin
P10109	0.8708452	0.2261987	9.122569	3.849912	0.0038093	0.0275460	Adrenodoxin, mitochondrial
Q9Y2D4	-1.5165389	0.3883525	8.669332	-3.905057	0.0038606	0.0277660	Exocyst complex component 6B
P27695	-1.4919668	0.3917033	9.367147	-3.808921	0.0038670	0.0277660	DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial
E5RK69	-1.1254137	0.2963630	9.367147	-3.797417	0.0039377	0.0281737	Annexin
Q96PK6	-0.9252023	0.2414472	9.065474	-3.831903	0.0039624	0.0282514	RNA-binding protein 14
Q9Y5U8	-2.4800568	0.6520455	9.266368	-3.803503	0.0039775	0.0282600	Mitochondrial pyruvate carrier 1
Q15738	-1.0818010	0.2856422	9.367147	-3.787259	0.0040012	0.0283289	Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
Q9BWJ5	-1.1786521	0.3118411	9.367147	-3.779657	0.0040494	0.0285708	Splicing factor 3B subunit 5
Q01581	-1.5736067	0.3810218	7.263324	-4.129965	0.0040656	0.0285856	Hydroxymethylglutaryl-CoA synthase, cytoplasmic
P62312	-1.5682756	0.4058757	8.681421	-3.863930	0.0040935	0.0286286	U6 snRNA-associated Sm-like protein LSm6
P31949	-0.9710473	0.2571969	9.319115	-3.775501	0.0041137	0.0286286	Protein S100-A11;Protein S100-A11, N-terminally processed
P04207	-1.4064185	0.3679024	8.920032	-3.822804	0.0041400	0.0286286	Ig kappa chain V-III region CLL
P78406	-1.6990379	0.3860063	6.247405	-4.401581	0.0041410	0.0286286	mRNA export factor
P49773	-0.9406572	0.2498222	9.367147	-3.765306	0.0041421	0.0286286	Histidine triad nucleotide-binding protein 1
P27169	-1.0408608	0.2721331	8.885189	-3.824822	0.0041573	0.0286362	Serum paraoxonase/arylesterase 1
Q13636	-1.9750968	0.4475759	6.180434	-4.412876	0.0041965	0.0288057	Ras-related protein Rab-31
Q96EM0	-1.2281296	0.3139364	8.247348	-3.912034	0.0042103	0.0288057	Trans-3-hydroxy-L-proline dehydratase
Q2TAY7	-1.0380001	0.2740571	9.062883	-3.787532	0.0042451	0.0289120	WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed
Q9BT09	-1.2017444	0.3172891	9.052006	-3.787537	0.0042543	0.0289120	Protein canopy homolog 3
P01699	-1.9617461	0.4491208	6.248678	-4.367970	0.0042972	0.0291062	Ig lambda chain V-I region VOR
P00488	-1.1450813	0.3056987	9.221528	-3.745784	0.0043915	0.0296460	Coagulation factor XIII A chain
Q04941	-1.3354806	0.3552239	9.068974	-3.759546	0.0044274	0.0297534	Proteolipid protein 2
P01611	-1.3210912	0.3549542	9.367147	-3.721864	0.0044367	0.0297534	Ig kappa chain V-I region Wes
P07360	-0.9508577	0.2503755	8.705608	-3.797726	0.0044970	0.0299248	Complement component C8 gamma chain
O75165	-0.7578962	0.2029469	9.178479	-3.734455	0.0045069	0.0299248	DnaJ homolog subfamily C member 13
Q9BXF6	-0.8964783	0.2416619	9.367147	-3.709638	0.0045234	0.0299248	Rab11 family-interacting protein 5
Q02818	-1.1067621	0.2686732	6.941836	-4.119362	0.0045442	0.0299248	Nucleobindin-1
Q9UNN8	-1.2379487	0.3234861	8.453236	-3.826899	0.0045465	0.0299248	Endothelial protein C receptor
Q96KP1	-1.0392328	0.2563691	7.214736	-4.053659	0.0045506	0.0299248	Exocyst complex component 2
P46063	-0.7705141	0.2065234	9.129952	-3.730880	0.0045745	0.0299851	ATP-dependent DNA helicase Q1
Q9HBL0	1.0363941	0.2703813	8.367147	3.833083	0.0045924	0.0299947	Tensin-1
P20042	-0.8792944	0.2360635	9.144030	-3.724821	0.0046055	0.0299947	Eukaryotic translation initiation factor 2 subunit 2
Q8IVD9	-0.9380220	0.2431161	8.145517	-3.858329	0.0046577	0.0301872	NudC domain-containing protein 3
Q13011	0.8580498	0.2280498	8.785364	3.762555	0.0046647	0.0301872	Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Q5JUQ0	2.8054144	0.6821194	6.810842	4.112791	0.0047732	0.0307912	Protein FAM78A
P10643	-1.1503065	0.3105456	9.106523	-3.704147	0.0047905	0.0308022	Complement component C7
Q9Y5U9	-0.9688010	0.2518567	8.060725	-3.846636	0.0048312	0.0308022	Immediate early response 3-interacting protein 1
P31689	-1.4848105	0.3869113	8.102049	-3.837599	0.0048469	0.0308022	DnaJ homolog subfamily A member 1
Q53GG5	1.0396066	0.2790314	8.862014	3.725770	0.0048582	0.0308022	PDZ and LIM domain protein 3
Q04837	-1.2706968	0.3379173	8.597962	-3.760378	0.0048649	0.0308022	Single-stranded DNA-binding protein, mitochondrial
Q9BU61	-1.2937160	0.3533023	9.367147	-3.661782	0.0048807	0.0308022	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3
Q9BXR6	-1.3408193	0.3662489	9.364182	-3.660951	0.0048897	0.0308022	Complement factor H-related protein 5
Q08357	-1.2512681	0.3308812	8.412243	-3.781623	0.0049038	0.0308022	Sodium-dependent phosphate transporter 2
Q9HCN8	-0.8376149	0.2283146	9.271872	-3.668688	0.0049114	0.0308022	Stromal cell-derived factor 2-like protein 1
Q8NDY3	1.2548368	0.3406687	9.012910	3.683452	0.0050360	0.0314298	[Protein ADP-ribosylarginine] hydrolase-like protein 1
P61020	-0.8349426	0.2252816	8.813746	-3.706218	0.0050537	0.0314298	Ras-related protein Rab-5B
P00918	-0.9493414	0.2601045	9.274179	-3.649846	0.0050579	0.0314298	Carbonic anhydrase 2
Q8TDB6	-0.9819803	0.2672639	9.048834	-3.674197	0.0050744	0.0314365	E3 ubiquitin-protein ligase DTX3L
P31994-2	-0.7713913	0.2103215	9.069055	-3.667677	0.0051068	0.0315412	Low affinity immunoglobulin gamma Fc region receptor II-b
Q8NBF2	-0.8115466	0.2231619	9.294232	-3.636582	0.0051468	0.0316076	NHL repeat-containing protein 2
O00299	-0.9153236	0.2514420	9.251612	-3.640298	0.0051558	0.0316076	Chloride intracellular channel protein 1
Q9UBI9	-1.9350473	0.4881801	7.178007	-3.963798	0.0051668	0.0316076	Headcase protein homolog
O75663	-1.6975991	0.4619708	8.936339	-3.674689	0.0051798	0.0316076	TIP41-like protein
Q9Y5J7	-1.4394711	0.3975506	9.367147	-3.620850	0.0052097	0.0316947	Mitochondrial import inner membrane translocase subunit Tim9
Q8WUM0	-0.7928646	0.2183894	9.223881	-3.630508	0.0052623	0.0319115	Nuclear pore complex protein Nup133
O15121	-1.3734454	0.3779119	9.175551	-3.634300	0.0052767	0.0319115	Sphingolipid delta(4)-desaturase DES1
P00742	-1.3361965	0.3240743	6.365924	-4.123118	0.0054529	0.0328791	Coagulation factor X;Factor X light chain;Factor X heavy chain;Activated factor Xa heavy chain
P46777	-1.0578875	0.2885954	8.703996	-3.665643	0.0054936	0.0330263	60S ribosomal protein L5
Q6P1L8	0.6856534	0.1900543	9.149544	3.607671	0.0055286	0.0331349	39S ribosomal protein L14, mitochondrial
P49756	-0.8733625	0.2438260	9.367147	-3.581909	0.0055442	0.0331349	RNA-binding protein 25
Q15493	-1.5865116	0.4375946	8.952542	-3.625528	0.0055726	0.0332070	Regucalcin
O00567	-1.6066654	0.4490482	9.292457	-3.577936	0.0056516	0.0335792	Nucleolar protein 56
Q9H4A6	-0.9863755	0.2760356	9.279941	-3.573364	0.0057052	0.0337990	Golgi phosphoprotein 3
Q6PCE3	-1.3068366	0.3388413	7.307566	-3.856780	0.0057433	0.0338422	Glucose 1,6-bisphosphate synthase
P24752	0.8145171	0.2252205	8.862587	3.616532	0.0057462	0.0338422	Acetyl-CoA acetyltransferase, mitochondrial
O15144	-1.0266458	0.2834041	8.798089	-3.622551	0.0057625	0.0338422	Actin-related protein 2/3 complex subunit 2
Q9Y646	-0.6906706	0.1939022	9.241032	-3.561953	0.0058489	0.0342504	Carboxypeptidase Q
Q1KMD3	-0.9588418	0.2678729	9.012210	-3.579466	0.0059227	0.0345833	Heterogeneous nuclear ribonucleoprotein U-like protein 2
P06396	-1.1557324	0.3165502	8.401875	-3.651024	0.0059642	0.0347206	Gelsolin
P56199	-0.8817502	0.2433638	8.590476	-3.623178	0.0059906	0.0347206	Integrin alpha-1
P62330	-0.7931556	0.2224860	9.069563	-3.564969	0.0059975	0.0347206	ADP-ribosylation factor 6
Q9HAN9	1.2305740	0.3215526	7.267944	3.826976	0.0060382	0.0347731	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Q96PE7	-1.1472298	0.3251398	9.367147	-3.528421	0.0060408	0.0347731	Methylmalonyl-CoA epimerase, mitochondrial
P17050	-0.9454418	0.2669981	9.102996	-3.541005	0.0061920	0.0355428	Alpha-N-acetylgalactosaminidase
Q9UBS4	-1.7470606	0.4933923	8.991571	-3.540916	0.0063144	0.0361080	DnaJ homolog subfamily B member 11
Q9H9B4	-0.7776690	0.2176464	8.705504	-3.573084	0.0063260	0.0361080	Sideroflexin-1
Q8TCJ2	-0.8698436	0.2449142	8.867863	-3.551625	0.0063478	0.0361307	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit STT3B
P62191	-1.0000517	0.2845274	9.148632	-3.514782	0.0064041	0.0363496	26S protease regulatory subunit 4
Q9Y5Z7	-1.9019574	0.4671525	6.063248	-4.071384	0.0064220	0.0363496	Host cell factor 2
P01597	-2.2333895	0.6337027	8.989760	-3.524349	0.0064826	0.0365908	Ig kappa chain V-I region DEE
P23284	-0.7744408	0.2195528	8.929246	-3.527355	0.0065208	0.0367045	Peptidyl-prolyl cis-trans isomerase B
P05062	-2.0647894	0.5510151	7.364182	-3.747246	0.0065595	0.0368200	Fructose-bisphosphate aldolase B
P60903	-0.8289441	0.2370600	9.148479	-3.496770	0.0065901	0.0368804	Protein S100-A10
O43920	0.8295850	0.2370882	9.111256	3.499056	0.0066074	0.0368804	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
Q68DH5	-0.9839434	0.2736703	8.291375	-3.595361	0.0066247	0.0368804	LMBR1 domain-containing protein 2
P08754	-1.0292580	0.2970275	9.367147	-3.465194	0.0066882	0.0369621	Guanine nucleotide-binding protein G(k) subunit alpha
O75643	-0.7286175	0.2103227	9.367147	-3.464284	0.0066980	0.0369621	U5 small nuclear ribonucleoprotein 200 kDa helicase
Q9HAV7	0.8532336	0.2444615	9.111332	3.490257	0.0067001	0.0369621	GrpE protein homolog 1, mitochondrial
P15848	0.9204565	0.2587469	8.517402	3.557363	0.0067121	0.0369621	Arylsulfatase B
P30050	-1.1309945	0.3250781	9.187400	-3.479147	0.0067338	0.0369812	60S ribosomal protein L12
P17540	0.9216483	0.2460734	7.245462	3.745420	0.0067728	0.0370568	Creatine kinase S-type, mitochondrial
P27797	-0.8755252	0.2533638	9.364182	-3.455605	0.0067957	0.0370568	Calreticulin
O14807	-0.9860449	0.2835156	9.124869	-3.477921	0.0068171	0.0370568	Ras-related protein M-Ras
O43290	-0.7436611	0.2153948	9.367147	-3.452549	0.0068261	0.0370568	U4/U6.U5 tri-snRNP-associated protein 1
P98160	-0.6944147	0.2001825	9.192685	-3.468908	0.0068387	0.0370568	Basement membrane-specific heparan sulfate proteoglycan core protein;Endorepellin;LG3 peptide
Q9GZY4	-1.6172207	0.4429828	7.722737	-3.650753	0.0068924	0.0371927	Cytochrome c oxidase assembly factor 1 homolog
Q16204	-0.7607082	0.2170148	8.802720	-3.505328	0.0069004	0.0371927	Coiled-coil domain-containing protein 6
Q14019	-2.3417241	0.5970824	6.367147	-3.921945	0.0069196	0.0371975	Coactosin-like protein
O75190-3	1.2231318	0.3561310	9.367147	3.434500	0.0070282	0.0375619	DnaJ homolog subfamily B member 6
Q9Y623	-1.9955095	0.5624933	8.346159	-3.547614	0.0070378	0.0375619	Myosin-4
P30101	-0.7361350	0.2143040	9.348665	-3.435003	0.0070429	0.0375619	Protein disulfide-isomerase A3
Q12907	-1.6602075	0.4672229	8.260767	-3.553352	0.0070944	0.0377376	Vesicular integral-membrane protein VIP36
O75533	-0.7480960	0.2181066	9.228009	-3.429955	0.0072371	0.0383531	Splicing factor 3B subunit 1
P21281	-1.3428216	0.3926852	9.324422	-3.419588	0.0072478	0.0383531	V-type proton ATPase subunit B, brain isoform
Q6ZVF9	-1.5316163	0.3683117	5.457648	-4.158478	0.0073162	0.0386145	G protein-regulated inducer of neurite outgrowth 3
P41208	-1.1048997	0.3218686	9.068594	-3.432766	0.0073920	0.0389135	Centrin-2
P32119	-0.8759792	0.2446675	7.843882	-3.580284	0.0074230	0.0389754	Peroxiredoxin-2
P55735	-0.9148870	0.2645561	8.692215	-3.458196	0.0075683	0.0395905	Protein SEC13 homolog
P56192	-1.0251690	0.2974781	8.777363	-3.446200	0.0075980	0.0395905	Methionine–tRNA ligase, cytoplasmic
Q5VUM1	0.7587056	0.2227429	9.160698	3.406195	0.0075986	0.0395905	Succinate dehydrogenase assembly factor 4, mitochondrial
Q8NBJ5	-1.0090957	0.2920463	8.660730	-3.455259	0.0076446	0.0396444	Procollagen galactosyltransferase 1
O43707	-1.3709413	0.3948639	8.501412	-3.471934	0.0076653	0.0396444	Alpha-actinin-4
P11021	-0.6930674	0.2026548	8.963582	-3.419941	0.0076742	0.0396444	78 kDa glucose-regulated protein
P02749	-0.9821379	0.2870910	8.943313	-3.420999	0.0076870	0.0396444	Beta-2-glycoprotein 1
Q92805	1.3677629	0.3988094	8.805419	3.429616	0.0077599	0.0398246	Golgin subfamily A member 1
Q96G03	-0.8738839	0.2590611	9.367147	-3.373274	0.0077611	0.0398246	Phosphoglucomutase-2
Q9UK41	-1.5562781	0.4608330	9.215373	-3.377097	0.0078939	0.0404039	Vacuolar protein sorting-associated protein 28 homolog
P61026	-0.8659400	0.2419636	7.548968	-3.578803	0.0079264	0.0404684	Ras-related protein Rab-10
P43686	-1.2985795	0.3872768	9.344890	-3.353104	0.0080462	0.0409144	26S protease regulatory subunit 6B
Q6Y288	-1.0690665	0.3176465	9.205175	-3.365585	0.0080540	0.0409144	Beta-1,3-glucosyltransferase
Q9BVG4	-1.4282890	0.4270284	9.366464	-3.344717	0.0081305	0.0411768	Protein PBDC1
Q9UBQ0	-1.1043560	0.3287140	9.186452	-3.359625	0.0081549	0.0411768	Vacuolar protein sorting-associated protein 29
Q6ICB0	-2.0382992	0.5475115	6.642201	-3.722843	0.0081665	0.0411768	Desumoylating isopeptidase 1
O60568	-1.0635431	0.3196281	9.367147	-3.327439	0.0083615	0.0419615	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Q5T447	-1.0258262	0.3034522	8.816996	-3.380520	0.0083634	0.0419615	E3 ubiquitin-protein ligase HECTD3
P17174	0.8269867	0.2470996	9.138666	3.346775	0.0083860	0.0419712	Aspartate aminotransferase, cytoplasmic
Q14011	-1.6060873	0.4676337	8.233933	-3.434499	0.0085160	0.0425171	Cold-inducible RNA-binding protein
Q9BSH5	-0.8065712	0.2403591	8.925093	-3.355692	0.0085470	0.0425675	Haloacid dehalogenase-like hydrolase domain-containing protein 3
Q9HCJ6	-0.8677868	0.2621467	9.364182	-3.310310	0.0086017	0.0427352	Synaptic vesicle membrane protein VAT-1 homolog-like
P16455	-0.7988054	0.2337057	8.298415	-3.417997	0.0086284	0.0427634	Methylated-DNA–protein-cysteine methyltransferase
Q9BX97	-1.3847012	0.3968670	7.704864	-3.489081	0.0087089	0.0429596	Plasmalemma vesicle-associated protein
Q96LD4	-2.0603233	0.5321719	5.834822	-3.871537	0.0087103	0.0429596	Tripartite motif-containing protein 47
P29992	-1.0018710	0.2947354	8.383031	-3.399222	0.0087449	0.0430256	Guanine nucleotide-binding protein subunit alpha-11
P05387	-0.7447264	0.2248658	9.208344	-3.311871	0.0087779	0.0430839	60S acidic ribosomal protein P2
P51692	-1.6950637	0.5100493	9.046817	-3.323333	0.0088295	0.0432328	Signal transducer and activator of transcription 5B
O60927	-0.9472893	0.2647292	7.019336	-3.578333	0.0089547	0.0437403	Protein phosphatase 1 regulatory subunit 11
A4D2B0	-1.7140517	0.5058492	8.313870	-3.388464	0.0089976	0.0437455	Metallo-beta-lactamase domain-containing protein 1
P16083	-1.0028849	0.2963950	8.355055	-3.383609	0.0089988	0.0437455	Ribosyldihydronicotinamide dehydrogenase [quinone]
Q13425	-0.7615654	0.2314925	9.254288	-3.289806	0.0090358	0.0438206	Beta-2-syntrophin
I3L505	1.1922390	0.3573203	8.688946	3.336611	0.0091461	0.0442499	Acyl carrier protein
Q9NX08	-0.7274661	0.2206251	8.945229	-3.297295	0.0093470	0.0450429	COMM domain-containing protein 8
Q96CN7	-1.0144660	0.3094016	9.138448	-3.278800	0.0093544	0.0450429	Isochorismatase domain-containing protein 1
O43592	-0.8026366	0.2463030	9.274135	-3.258736	0.0094762	0.0454937	Exportin-T
Q8N392	2.3552996	0.6371851	6.218828	3.696413	0.0095013	0.0454937	Rho GTPase-activating protein 18
P01621	-1.1890923	0.3617796	8.937835	-3.286787	0.0095152	0.0454937	Ig kappa chain V-III region NG9
Q9UMR3	-1.6328959	0.4711525	7.367147	-3.465748	0.0096580	0.0460681	T-box transcription factor TBX20
P35754	0.8371729	0.2577782	9.203352	3.247648	0.0097456	0.0463770	Glutaredoxin-1
O60503	1.2572380	0.3410034	6.154065	3.686878	0.0097933	0.0464953	Adenylate cyclase type 9
Q13825	1.3948092	0.4331181	9.367147	3.220391	0.0099586	0.0471699	Methylglutaconyl-CoA hydratase, mitochondrial
O95159	-1.7663091	0.5271198	8.007934	-3.350868	0.0100529	0.0475059	Zinc finger protein-like 1
Q8IWU2	-0.7035098	0.2110669	8.106368	-3.333113	0.0101436	0.0477336	Serine/threonine-protein kinase LMTK2
Q6B0K9	-1.3448839	0.3993105	7.801037	-3.368015	0.0101825	0.0477336	Hemoglobin subunit mu
Q13541	0.9175109	0.2861836	9.367147	3.206022	0.0101958	0.0477336	Eukaryotic translation initiation factor 4E-binding protein 1
Q6UXG3	1.6474617	0.5119132	9.212796	3.218244	0.0102080	0.0477336	CMRF35-like molecule 9
P03915	-1.1507202	0.3487844	8.364164	-3.299231	0.0102186	0.0477336	NADH-ubiquinone oxidoreductase chain 5
P14174	-0.8418646	0.2604069	8.971113	-3.232881	0.0103182	0.0480886	Macrophage migration inhibitory factor
P34947	-1.4080509	0.4397174	9.308356	-3.202173	0.0103422	0.0480898	G protein-coupled receptor kinase 5
O75436	-0.9929865	0.3057783	8.698092	-3.247407	0.0105014	0.0487127	Vacuolar protein sorting-associated protein 26A
P19474	-1.1365988	0.3407495	7.877271	-3.335584	0.0105291	0.0487127	E3 ubiquitin-protein ligase TRIM21
O14656	-1.8183830	0.5547207	8.367147	-3.278015	0.0105509	0.0487127	Torsin-1A
Q08AG7	-1.1984106	0.3483040	7.108164	-3.440703	0.0105720	0.0487127	Mitotic-spindle organizing protein 1
P05060	-2.3136323	0.6780046	7.260747	-3.412414	0.0106399	0.0488839	Secretogranin-1;PE-11;GAWK peptide;CCB peptide
Q08211	-0.6963521	0.2190285	9.364182	-3.179276	0.0106573	0.0488839	ATP-dependent RNA helicase A
Q0VAK6	1.1733962	0.3600710	8.439565	3.258791	0.0107412	0.0491581	Leiomodin-3
P51665	-0.7816374	0.2455892	9.244310	-3.182703	0.0107689	0.0491739	26S proteasome non-ATPase regulatory subunit 7
Q9H2J4	-0.8248510	0.2600959	9.364182	-3.171334	0.0107971	0.0491921	Phosducin-like protein 3
Q8IWB7	1.6050991	0.4817240	7.755733	3.331989	0.0108235	0.0492022	WD repeat and FYVE domain-containing protein 1
P51970	0.7463947	0.2339094	9.051112	3.190956	0.0109113	0.0494190	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Q15691	-0.9045387	0.2773216	8.309540	-3.261696	0.0109198	0.0494190	Microtubule-associated protein RP/EB family member 1

4.6 Interaction

4.6.1 Volcano-plot

volcanoInt <- ggplot(rowData(pe[["proteinRobust"]])$"locationR:tissueV",
                 aes(x = logFC, y = -log10(pval), color = adjPval < 0.05)) +
 geom_point(cex = 2.5) +
 scale_color_manual(values = alpha(c("black", "red"), 0.5)) + theme_minimal()
volcanoInt

4.6.2 Heatmap

There were no genes significant at the 5% FDR level. We return the top 25 genes.

sigNamesInt <- rowData(pe[["proteinRobust"]])$"locationR:tissueV" %>%
 rownames_to_column("proteinRobust") %>%
 filter(adjPval<0.05) %>%
 pull(proteinRobust)
hlp <- order((rowData(pe[["proteinRobust"]])$"locationR:tissueV")[,"adjPval"])[1:25]
heatmap(assay(pe[["proteinRobust"]])[hlp, ])

There are 0 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"locationR:tissueV" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  filter(adjPval<0.05) %>%
  arrange(pval)

5 Large difference in number of proteins that are returned

Note, that much more proteins are returned significant for average contrast (\(\log_2 FC_{V-A}\)) as compared to contrast for assessing the fold change between ventriculum and atrium left and right. The power for the average contrast is larger than for the contrast left or right because the log2 FC can be estimated with higher precision.

For none of the proteins the interaction was significant (change in log2 FC between ventriculum and atrium in the right vs the left heart region). The power for the interaction is typically low.

5.1 Reason

Part of variance covariance matrix of model parameters due to design:

X <- model.matrix(~ location*tissue + patient, colData(pe))
covarUnscaled <- solve(t(X) %*% X)

Variance of contrasts (diagonal elements) due to design

varContrasts <- t(L)%*%covarUnscaled%*%L %>%
  diag
varContrasts

##                           tissueV       tissueV + locationR:tissueV 
##                         0.6666667                         0.6666667 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.3333333                         1.3333333

sqrt(varContrasts)

##                           tissueV       tissueV + locationR:tissueV 
##                         0.8164966                         0.8164966 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.5773503                         1.1547005

So it is clear that the standard error of the log2 FC left and right is the same. That of the average contrast is a factor \(\sqrt{2}\) smaller! Indeed, we use double the number of samples to estimate it!

varContrasts[3]/varContrasts[2]

## tissueV + 0.5 * locationR:tissueV 
##                               0.5

sqrt(varContrasts)[3]/sqrt(varContrasts)[2]

## tissueV + 0.5 * locationR:tissueV 
##                         0.7071068

1/sqrt(2)

## [1] 0.7071068

The standard error of the interaction is a factor \(\sqrt{2}\) larger than that of the main effects!

varContrasts[4]/varContrasts[2]

## locationR:tissueV 
##                 2

sqrt(varContrasts)[4]/sqrt(varContrasts)[2]

## locationR:tissueV 
##          1.414214

sqrt(2)

## [1] 1.414214

5.2 Msqrob

This is not the case for the standard errors of protein 2???

rowData(pe[["proteinRobust"]])$"tissueV"[2,]

rowData(pe[["proteinRobust"]])$"tissueV + locationR:tissueV"[2,]

rowData(pe[["proteinRobust"]])$"tissueV + 0.5 * locationR:tissueV"[2,]

rowData(pe[["proteinRobust"]])$"locationR:tissueV"[2,]

Because msqrob is using robust regression to assess DE!

pe %>%
  colData %>%
  as_tibble %>%
  mutate(w=getModel(rowData(pe[["proteinRobust"]])$msqrobModels[[2]])$w)

For protein 2 the samples at the left and right side have different weights!

5.2.1 Part of standard error due to design:

covUnscaledRobust <- solve(
  t(X) %*%
  diag(
    getModel(rowData(pe[["proteinRobust"]])$msqrobModels[[2]])$w) %*% X)

varContrastsRobust <- t(L)%*%covUnscaledRobust%*%L %>%
  diag
varContrastsRobust

##                           tissueV       tissueV + locationR:tissueV 
##                         0.7161526                         0.8673176 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.3937862                         1.5917957

sqrt(varContrastsRobust)

##                           tissueV       tissueV + locationR:tissueV 
##                         0.8462580                         0.9312989 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.6275239                         1.2616639

5.2.2 Standard errors Contrasts

sqrt(varContrastsRobust) * getSigmaPosterior(rowData(pe[["proteinRobust"]])$msqrobModels[[2]])

##                           tissueV       tissueV + locationR:tissueV 
##                         0.5564990                         0.6124218 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.4126595                         0.8296697

rowData(pe[["proteinRobust"]])$"tissueV"[2,]

rowData(pe[["proteinRobust"]])$"tissueV + locationR:tissueV"[2,]

rowData(pe[["proteinRobust"]])$"tissueV + 0.5 * locationR:tissueV"[2,]

rowData(pe[["proteinRobust"]])$"locationR:tissueV"[2,]

5.3 Stagewise testing

stageR paper

5.3.1 Omnibus test

source("https://raw.githubusercontent.com/statOmics/SGA2020/gh-pages/assets/topFeaturesOmnibus.R")
pe <- omnibusTest(pe, "proteinRobust", L)

5.3.2 Heatmap significant proteins Omnibus test

We first select the names of the proteins that were declared signficant.

sigNamesOmnibus <- rowData(pe[["proteinRobust"]])$omnibusTest %>%
 rownames_to_column("proteinRobust") %>%
 filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesOmnibus, ])

There are 260 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$omnibusTest  %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)

	tissueV	tissueV…locationR.tissueV	tissueV…0.5…locationR.tissueV	locationR.tissueV	df1	df2	Fstat	pval	adjPval	rowData(pe[[“proteinRobust”]])$Protein.names
P08590	7.9679512	5.5038377	6.7358945	-2.4641135	2	9.367147	244.991757	0.0000000	0.0000166	Myosin light chain 3
P12883	4.6698827	1.9691001	3.3194914	-2.7007826	2	9.181668	93.450626	0.0000008	0.0008004	Myosin-7
P10916	6.9261087	2.9211752	4.9236420	-4.0049335	2	7.367147	104.165735	0.0000040	0.0022692	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
O75368	-2.2715945	-1.8193257	-2.0454601	0.4522688	2	9.289260	57.744593	0.0000058	0.0022692	SH3 domain-binding glutamic acid-rich-like protein
P06858	1.7891922	3.3546738	2.5719330	1.5654816	2	9.249267	57.263295	0.0000062	0.0022692	Lipoprotein lipase
Q6UWY5	-3.2536428	-2.4568740	-2.8552584	0.7967688	2	9.113260	57.689121	0.0000067	0.0022692	Olfactomedin-like protein 1
P46821	-2.1668803	-1.6065386	-1.8867094	0.5603417	2	9.367147	52.493381	0.0000081	0.0023629	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P21810	-3.2145420	-2.9247828	-3.0696624	0.2897592	2	8.756796	54.846099	0.0000111	0.0028317	Biglycan
P05546	-1.9318824	-1.7278000	-1.8298412	0.2040825	2	9.271661	45.743962	0.0000157	0.0033853	Heparin cofactor 2
P35442	-2.3010500	-3.2464603	-2.7737551	-0.9454102	2	8.367147	53.231275	0.0000174	0.0033853	Thrombospondin-2
P29622	-2.1134793	-1.8479195	-1.9806994	0.2655598	2	9.367147	43.397164	0.0000183	0.0033853	Kallistatin
Q06828	-4.2030186	-4.1220908	-4.1625547	0.0809278	2	8.969004	41.115768	0.0000304	0.0048304	Fibromodulin
Q8N474	-3.3090235	-2.1085362	-2.7087798	1.2004873	2	7.897481	50.827857	0.0000309	0.0048304	Secreted frizzled-related protein 1
P13533	-4.0404076	-3.8883168	-3.9643622	0.1520908	2	9.098373	38.029280	0.0000382	0.0054877	Myosin-6
O95865	-2.1732192	-1.0065234	-1.5898713	1.1666958	2	9.367147	35.906256	0.0000405	0.0054877	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
P02776	-1.7615098	-2.8183635	-2.2899367	-1.0568537	2	7.975973	44.012604	0.0000491	0.0061323	Platelet factor 4;Platelet factor 4, short form
O94875-10	2.3744000	1.3908537	1.8826268	-0.9835463	2	8.904913	36.481141	0.0000513	0.0061323	Sorbin and SH3 domain-containing protein 2
A6NMZ7	-2.2762344	-3.0708477	-2.6735410	-0.7946133	2	9.367147	32.942459	0.0000578	0.0062043	Collagen alpha-6(VI) chain
Q9UGT4	-2.3006162	-2.4431450	-2.3718806	-0.1425288	2	9.191824	33.292465	0.0000616	0.0062043	Sushi domain-containing protein 2
Q9ULD0	-0.5053595	-3.5759065	-2.0406330	-3.0705471	2	7.367147	45.894024	0.0000694	0.0062043	2-oxoglutarate dehydrogenase-like, mitochondrial
P02452	-2.9630153	-1.8165071	-2.3897612	1.1465082	2	8.292268	37.461372	0.0000704	0.0062043	Collagen alpha-1(I) chain
Q16647	-2.7991521	-1.5254456	-2.1622988	1.2737065	2	9.028244	32.827062	0.0000721	0.0062043	Prostacyclin synthase
Q14764	-1.6267934	-1.6082319	-1.6175126	0.0185614	2	9.367147	31.133799	0.0000728	0.0062043	Major vault protein
P51884	-2.1343314	-1.3860414	-1.7601864	0.7482899	2	9.157371	32.051859	0.0000733	0.0062043	Lumican
P14854	2.4019126	1.0484630	1.7251878	-1.3534497	2	8.431469	35.721385	0.0000764	0.0062130	Cytochrome c oxidase subunit 6B1
Q9ULL5-3	-3.4165405	-1.1847929	-2.3006667	2.2317476	2	7.846127	39.499014	0.0000802	0.0062470	Proline-rich protein 12
P24844	-2.4962161	-1.7674609	-2.1318385	0.7287552	2	9.311934	30.378458	0.0000830	0.0062470	Myosin regulatory light polypeptide 9
Q9P2B2	-2.0393915	-2.0352257	-2.0373086	0.0041657	2	9.367147	29.832341	0.0000866	0.0062811	Prostaglandin F2 receptor negative regulator
O43677	-2.7199107	-2.9699638	-2.8449373	-0.2500530	2	8.430596	33.880901	0.0000933	0.0063582	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q15113	-2.7424988	-1.9598986	-2.3511987	0.7826003	2	9.185821	29.999135	0.0000939	0.0063582	Procollagen C-endopeptidase enhancer 1
P54652	-1.5932853	-2.7266813	-2.1599833	-1.1333960	2	9.078544	29.823495	0.0001022	0.0066163	Heat shock-related 70 kDa protein 2
P18428	-1.9996058	-1.6908752	-1.8452405	0.3087306	2	9.138659	29.420581	0.0001042	0.0066163	Lipopolysaccharide-binding protein
P51888	-3.0081810	-1.8386140	-2.4233975	1.1695670	2	7.159338	41.006660	0.0001199	0.0073856	Prolargin
P00748	-1.9914680	-1.9153262	-1.9533971	0.0761418	2	9.103103	27.313642	0.0001423	0.0081123	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q9BW30	-2.7245919	-2.3265968	-2.5255943	0.3979951	2	8.999217	27.647870	0.0001437	0.0081123	Tubulin polymerization-promoting protein family member 3
P02775	-1.9622566	-2.2055428	-2.0838997	-0.2432862	2	9.367147	26.290147	0.0001437	0.0081123	Platelet basic protein;Connective tissue-activating peptide III;TC-2;Connective tissue-activating peptide III(1-81);Beta-thromboglobulin;Neutrophil-activating peptide 2(74);Neutrophil-activating peptide 2(73);Neutrophil-activating peptide 2;TC-1;Neutrophil-activating peptide 2(1-66);Neutrophil-activating peptide 2(1-63)
P48681	-1.3334013	-1.4912879	-1.4123446	-0.1578867	2	9.364182	25.850082	0.0001539	0.0084432	Nestin
P08294	-2.7503241	-1.8848664	-2.3175953	0.8654577	2	7.961617	31.908193	0.0001579	0.0084432	Extracellular superoxide dismutase [Cu-Zn]
O00180	-4.2526703	-4.6213080	-4.4369891	-0.3686377	2	8.367147	28.998202	0.0001728	0.0090023	Potassium channel subfamily K member 1
P02743	-2.1700557	-1.5947113	-1.8823835	0.5753443	2	9.367147	24.487777	0.0001903	0.0095261	Serum amyloid P-component;Serum amyloid P-component(1-203)
Q92508	4.0552373	3.0309383	3.5430878	-1.0242991	2	6.367147	42.896980	0.0002019	0.0095261	Piezo-type mechanosensitive ion channel component 1
Q53GQ0	-2.4232423	-1.2106156	-1.8169289	1.2126267	2	9.357570	24.036931	0.0002057	0.0095261	Very-long-chain 3-oxoacyl-CoA reductase
P01031	-1.3157564	-1.6265238	-1.4711401	-0.3107674	2	8.491718	26.981232	0.0002093	0.0095261	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
P23083	-4.2325442	-2.2876958	-3.2601200	1.9448484	2	7.367147	32.815851	0.0002143	0.0095261	Ig heavy chain V-I region V35
P28066	-1.1656689	-2.1768243	-1.6712466	-1.0111554	2	8.729782	25.864797	0.0002145	0.0095261	Proteasome subunit alpha type-5
P00325	-2.1119462	-0.8948669	-1.5034066	1.2170793	2	8.984001	24.852199	0.0002181	0.0095261	Alcohol dehydrogenase 1B
P36955	-2.3377901	-1.0488427	-1.6933164	1.2889474	2	8.143555	28.131132	0.0002203	0.0095261	Pigment epithelium-derived factor
P07451	-1.8489373	-0.7177006	-1.2833190	1.1312367	2	9.367147	23.447331	0.0002256	0.0095504	Carbonic anhydrase 3
Q8TBQ9	-2.8189960	-0.6775596	-1.7482778	2.1414364	2	8.622892	25.696103	0.0002329	0.0096576	Protein kish-A
P46060	-1.9620904	-1.4474474	-1.7047689	0.5146430	2	8.367147	25.515065	0.0002748	0.0108656	Ran GTPase-activating protein 1
P05997	-3.0856148	-2.0117308	-2.5486728	1.0738840	2	8.940173	23.497890	0.0002756	0.0108656	Collagen alpha-2(V) chain
Q5NDL2	-2.2948242	-2.7081295	-2.5014769	-0.4133053	2	8.664509	24.342702	0.0002781	0.0108656	EGF domain-specific O-linked N-acetylglucosamine transferase
P60468	-1.4647431	-2.4380224	-1.9513827	-0.9732794	2	8.222346	25.660429	0.0002918	0.0110366	Protein transport protein Sec61 subunit beta
P35625	-1.9975691	-3.9383116	-2.9679404	-1.9407425	2	7.940282	26.775492	0.0002956	0.0110366	Metalloproteinase inhibitor 3
Q9UBG0	-2.5547510	-0.7142782	-1.6345146	1.8404728	2	9.172396	22.329358	0.0002987	0.0110366	C-type mannose receptor 2
P36021	-3.1085951	-1.8982919	-2.5034435	1.2103032	2	8.367147	24.359698	0.0003244	0.0115591	Monocarboxylate transporter 8
Q15327	-1.3451694	-2.2030029	-1.7740861	-0.8578335	2	9.236415	21.635546	0.0003270	0.0115591	Ankyrin repeat domain-containing protein 1
Q8TBP6	-1.9233155	-1.4935775	-1.7084465	0.4297380	2	8.978834	22.283528	0.0003299	0.0115591	Solute carrier family 25 member 40
Q6PCB0	-1.3038737	-2.3288520	-1.8163629	-1.0249783	2	8.934041	22.269633	0.0003379	0.0116359	von Willebrand factor A domain-containing protein 1
Q69YU5	1.7571878	3.2547381	2.5059630	1.4975503	2	8.695422	22.797308	0.0003481	0.0117889	Uncharacterized protein C12orf73
Q14195-2	-2.5380012	-1.9689229	-2.2534620	0.5690783	2	9.230176	21.170148	0.0003562	0.0118643	Dihydropyrimidinase-related protein 3
O14980	-1.2169774	-1.0123912	-1.1146843	0.2045863	2	9.367147	19.759032	0.0004357	0.0142084	Exportin-1
P30405	-1.5177122	-1.8429377	-1.6803249	-0.3252255	2	9.367147	19.667148	0.0004435	0.0142084	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q92604	-2.2504519	-1.9059820	-2.0782169	0.3444699	2	9.299173	19.769875	0.0004475	0.0142084	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
Q8WWA0	-5.8725166	-3.0334649	-4.4529908	2.8390517	2	8.102804	22.849873	0.0004667	0.0144071	Intelectin-1
P41240	-1.5466953	-1.1222942	-1.3344948	0.4244011	2	8.997098	20.197105	0.0004711	0.0144071	Tyrosine-protein kinase CSK
P04004	-1.6269790	-1.9085091	-1.7677440	-0.2815301	2	8.731887	20.771990	0.0004795	0.0144071	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P04083	-1.5201990	-1.1641919	-1.3421955	0.3560071	2	9.367147	19.236503	0.0004821	0.0144071	Annexin A1
Q7L4S7	-1.7124303	-2.5146192	-2.1135247	-0.8021888	2	7.099840	26.061963	0.0005366	0.0158023	Protein ARMCX6
Q9BXN1	-2.6634064	-1.9082906	-2.2858485	0.7551159	2	8.959110	19.485646	0.0005462	0.0158547	Asporin
Q15274	-1.9285076	-2.1429004	-2.0357040	-0.2143928	2	7.862886	22.235599	0.0005803	0.0164135	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q6YN16	1.5603531	1.5530695	1.5567113	-0.0072836	2	9.367147	18.297605	0.0005816	0.0164135	Hydroxysteroid dehydrogenase-like protein 2
Q07954	-1.6573532	-0.9345645	-1.2959588	0.7227887	2	9.367147	18.225418	0.0005902	0.0164290	Prolow-density lipoprotein receptor-related protein 1;Low-density lipoprotein receptor-related protein 1 85 kDa subunit;Low-density lipoprotein receptor-related protein 1 515 kDa subunit;Low-density lipoprotein receptor-related protein 1 intracellular domain
Q9NZ01	-2.4109216	-1.3161577	-1.8635396	1.0947640	2	8.632777	19.496331	0.0006289	0.0172694	Very-long-chain enoyl-CoA reductase
P12110	-1.9881397	-1.1989195	-1.5935296	0.7892202	2	8.169020	20.611857	0.0006427	0.0174119	Collagen alpha-2(VI) chain
O15230	-1.4246624	-1.3242727	-1.3744676	0.1003897	2	8.636336	19.184672	0.0006647	0.0175993	Laminin subunit alpha-5
P04003	-1.5009188	-1.3710495	-1.4359842	0.1298693	2	8.969835	18.393299	0.0006701	0.0175993	C4b-binding protein alpha chain
Q9Y6X5	-1.3875045	-1.5311540	-1.4593292	-0.1436495	2	8.651882	18.893138	0.0006968	0.0175993	Bis(5-adenosyl)-triphosphatase ENPP4
O95980	-2.5277905	-1.3310519	-1.9294212	1.1967386	2	8.146506	20.131018	0.0007039	0.0175993	Reversion-inducing cysteine-rich protein with Kazal motifs
Q9NRG4	2.1716027	2.6224932	2.3970480	0.4508904	2	8.367147	19.399707	0.0007209	0.0175993	N-lysine methyltransferase SMYD2
P14550	-1.3982496	-1.2114057	-1.3048277	0.1868439	2	8.802749	18.359099	0.0007231	0.0175993	Alcohol dehydrogenase [NADP(+)]
P23434	1.1390966	1.4064762	1.2727864	0.2673796	2	9.367147	17.202826	0.0007310	0.0175993	Glycine cleavage system H protein, mitochondrial
P23142	-1.8155347	-2.7792347	-2.2973847	-0.9637000	2	7.535834	21.837282	0.0007315	0.0175993	Fibulin-1
Q96LL9	-2.4127080	-0.0753563	-1.2440322	2.3373517	2	8.757117	18.375128	0.0007348	0.0175993	DnaJ homolog subfamily C member 30
P49207	-1.5105253	-1.2315384	-1.3710319	0.2789869	2	8.971215	17.916007	0.0007362	0.0175993	60S ribosomal protein L34
Q9UL18	-2.6225313	-0.0143926	-1.3184619	2.6081387	2	7.860316	20.522524	0.0007582	0.0179146	Protein argonaute-1
Q9BUF5	-1.9157084	-1.6208543	-1.7682813	0.2948542	2	9.247853	17.096107	0.0007824	0.0181189	Tubulin beta-6 chain
Q5JPH6	3.5281305	3.2877733	3.4079519	-0.2403572	2	5.776077	31.445071	0.0007853	0.0181189	Probable glutamate–tRNA ligase, mitochondrial
P04196	-1.9303128	-1.4451224	-1.6877176	0.4851904	2	7.453131	21.582819	0.0007936	0.0181189	Histidine-rich glycoprotein
Q9BZH6	1.8880941	3.4428053	2.6654497	1.5547112	2	8.320379	18.870664	0.0008094	0.0182743	WD repeat-containing protein 11
P30711	-1.2732431	-2.3217401	-1.7974916	-1.0484970	2	9.037365	17.194858	0.0008309	0.0183797	Glutathione S-transferase theta-1
P48163	-0.9106484	-2.9597295	-1.9351889	-2.0490811	2	7.571810	20.855204	0.0008322	0.0183797	NADP-dependent malic enzyme
O60760	-3.5990151	-0.9397549	-2.2693850	2.6592602	2	8.367147	18.293167	0.0008815	0.0192599	Hematopoietic prostaglandin D synthase
Q9UHG2	-1.5559341	-3.1758055	-2.3658698	-1.6198713	2	8.844100	17.122052	0.0009098	0.0196037	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
P04275	-1.0410359	-1.3527637	-1.1968998	-0.3117278	2	8.942806	16.900421	0.0009165	0.0196037	von Willebrand factor;von Willebrand antigen 2
O75828	-1.6544202	-1.3281193	-1.4912698	0.3263009	2	9.367147	15.998460	0.0009528	0.0201685	Carbonyl reductase [NADPH] 3
Q9UBB5	2.7451793	0.1324247	1.4388020	-2.6127546	2	6.367147	24.825998	0.0009851	0.0202862	Methyl-CpG-binding domain protein 2
Q92736-2	-3.3064395	1.1050323	-1.1007036	4.4114718	2	8.713491	16.861662	0.0010105	0.0202862	Ryanodine receptor 2
O00264	-1.9731043	-0.8423921	-1.4077482	1.1307122	2	9.044168	16.227446	0.0010183	0.0202862	Membrane-associated progesterone receptor component 1
O14967	-2.3785961	-0.8680171	-1.6233066	1.5105790	2	8.527297	17.184767	0.0010199	0.0202862	Calmegin
P40261	-2.3445730	-0.5432505	-1.4439118	1.8013225	2	9.220700	15.909097	0.0010245	0.0202862	Nicotinamide N-methyltransferase
P24298	1.2985007	1.9913967	1.6449487	0.6928960	2	8.587983	17.026685	0.0010272	0.0202862	Alanine aminotransferase 1
Q86WV6	-1.0472162	-1.3102966	-1.1787564	-0.2630805	2	9.222627	15.868371	0.0010332	0.0202862	Stimulator of interferon genes protein
P07357	-1.1425305	-1.2392930	-1.1909118	-0.0967626	2	9.209682	15.867195	0.0010383	0.0202862	Complement component C8 alpha chain
Q8WZA9	-1.4960398	-0.6736916	-1.0848657	0.8223482	2	9.178039	15.739712	0.0010807	0.0209140	Immunity-related GTPase family Q protein
P11586	0.5339844	2.0133011	1.2736427	1.4793167	2	7.995663	17.874183	0.0011203	0.0211071	C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
Q92681	-2.1962163	-1.4142146	-1.8052155	0.7820017	2	7.879124	18.144950	0.0011238	0.0211071	Regulatory solute carrier protein family 1 member 1
Q53GG5-2	-2.9088697	-1.9710170	-2.4399434	0.9378527	2	8.356632	16.953171	0.0011449	0.0211071	PDZ and LIM domain protein 3
P49458	-2.2735269	-1.4838150	-1.8786710	0.7897119	2	7.198623	20.014977	0.0011469	0.0211071	Signal recognition particle 9 kDa protein
Q00G26	0.9979847	1.9641232	1.4810539	0.9661385	2	7.550595	18.910476	0.0011476	0.0211071	Perilipin-5
P62760	-1.9146688	-1.8349672	-1.8748180	0.0797016	2	9.106554	15.565960	0.0011530	0.0211071	Visinin-like protein 1
P01024	-1.1180307	-1.1402588	-1.1291448	-0.0222281	2	9.104573	15.482574	0.0011758	0.0212548	Complement C3;Complement C3 beta chain;C3-beta-c;Complement C3 alpha chain;C3a anaphylatoxin;Acylation stimulating protein;Complement C3b alpha chain;Complement C3c alpha chain fragment 1;Complement C3dg fragment;Complement C3g fragment;Complement C3d fragment;Complement C3f fragment;Complement C3c alpha chain fragment 2
Q92930	-0.1213121	-2.8336656	-1.4774889	-2.7123535	2	7.608745	18.515276	0.0011932	0.0212548	Ras-related protein Rab-8B
Q9UQ35	-1.3570787	-1.0924340	-1.2247564	0.2646447	2	9.347887	15.033331	0.0011996	0.0212548	Serine/arginine repetitive matrix protein 2
Q9UNW9	4.0122337	2.5998314	3.3060326	-1.4124023	2	9.088964	15.387063	0.0012083	0.0212548	RNA-binding protein Nova-2
Q9HCB6	-1.7783135	-2.4125154	-2.0954145	-0.6342019	2	8.640884	16.083904	0.0012223	0.0212548	Spondin-1
P12814	-1.6827515	-2.1204665	-1.9016090	-0.4377150	2	8.156643	17.035633	0.0012238	0.0212548	Alpha-actinin-1
P02747	-2.6697776	-1.0364223	-1.8530999	1.6333553	2	6.990471	20.199403	0.0012441	0.0214237	Complement C1q subcomponent subunit C
Q5M9N0	-3.5146838	-2.0022131	-2.7584485	1.5124707	2	8.332430	16.540082	0.0012555	0.0214382	Coiled-coil domain-containing protein 158
P50453	-1.0174286	-1.3982165	-1.2078225	-0.3807879	2	8.945377	15.376873	0.0012745	0.0215714	Serpin B9
Q53T59	-1.8461756	-1.7698451	-1.8080103	0.0763306	2	7.984426	17.164039	0.0012845	0.0215714	HCLS1-binding protein 3
Q6SZW1	-2.6395602	-1.5070061	-2.0732831	1.1325541	2	7.367147	18.667082	0.0013052	0.0216831	Sterile alpha and TIR motif-containing protein 1
Q9Y3B4	-1.2603707	-1.3147360	-1.2875533	-0.0543653	2	9.015209	15.110736	0.0013210	0.0216831	Splicing factor 3B subunit 6
P25940	-1.7454125	-1.5404072	-1.6429098	0.2050053	2	9.102407	14.972850	0.0013232	0.0216831	Collagen alpha-3(V) chain
P07585	-1.9253602	-2.3393141	-2.1323372	-0.4139540	2	9.206541	14.779272	0.0013365	0.0217264	Decorin
P19429	2.3063639	2.1668090	2.2365865	-0.1395550	2	8.157979	16.529335	0.0013504	0.0217783	Troponin I, cardiac muscle
O43464	-1.9028432	0.7561617	-0.5733408	2.6590048	2	9.113486	14.824580	0.0013647	0.0218337	Serine protease HTRA2, mitochondrial
P08603	-0.8116849	-1.4843140	-1.1479994	-0.6726292	2	9.367147	14.439646	0.0013753	0.0218337	Complement factor H
O94919	-1.1247209	-1.1348303	-1.1297756	-0.0101094	2	9.130892	14.463629	0.0014782	0.0230492	Endonuclease domain-containing 1 protein
Q8WY22	-1.8091979	-1.2056646	-1.5074312	0.6035334	2	8.367147	15.677943	0.0014790	0.0230492	BRI3-binding protein
Q9ULC3	-1.6333020	-1.2294459	-1.4313739	0.4038561	2	8.667470	15.138524	0.0014859	0.0230492	Ras-related protein Rab-23
Q92621	-1.7036447	-0.7416850	-1.2226648	0.9619598	2	9.364182	14.030843	0.0015233	0.0234259	Nuclear pore complex protein Nup205
Q9H1K0	-0.9671803	-2.2373739	-1.6022771	-1.2701936	2	7.367147	17.710998	0.0015333	0.0234259	Rabenosyn-5
P01008	-1.5692162	-1.5215811	-1.5453986	0.0476351	2	9.323357	13.999194	0.0015554	0.0235870	Antithrombin-III
Q9BUH6	-0.6802448	-1.4854844	-1.0828646	-0.8052395	2	9.143080	14.095348	0.0016097	0.0242290	Protein PAXX
Q9BTV4	-1.8099873	-1.3789318	-1.5944595	0.4310554	2	9.158605	13.815891	0.0017161	0.0255520	Transmembrane protein 43
Q09161	1.5693007	2.3707165	1.9700086	0.8014158	2	6.160511	21.233004	0.0017227	0.0255520	Nuclear cap-binding protein subunit 1
Q9BS26	-1.2463986	-1.1124513	-1.1794250	0.1339473	2	9.301620	13.544340	0.0017568	0.0258690	Endoplasmic reticulum resident protein 44
P31994-2	-1.5795166	0.0367340	-0.7713913	1.6162506	2	9.069055	13.731805	0.0018033	0.0262785	Low affinity immunoglobulin gamma Fc region receptor II-b
P14543	-1.4365423	-1.3099501	-1.3732462	0.1265922	2	9.100089	13.669602	0.0018134	0.0262785	Nidogen-1
Q12996	-2.0094808	-1.2430859	-1.6262833	0.7663949	2	6.440629	19.607714	0.0018235	0.0262785	Cleavage stimulation factor subunit 3
P01699	-4.3035389	0.3800467	-1.9617461	4.6835856	2	6.248678	20.192672	0.0018738	0.0267402	Ig lambda chain V-I region VOR
Q6PI78	1.1088321	1.9756926	1.5422623	0.8668605	2	9.038962	13.581367	0.0018902	0.0267402	Transmembrane protein 65
Q2TAA5	-1.2916274	-0.9391581	-1.1153927	0.3524693	2	9.181244	13.392881	0.0018956	0.0267402	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
P35052	-0.6292316	-1.9653657	-1.2972987	-1.3361341	2	7.794113	15.536092	0.0019081	0.0267402	Glypican-1;Secreted glypican-1
Q9NY15	-2.1436460	-0.7334760	-1.4385610	1.4101701	2	9.350476	13.075610	0.0019548	0.0272061	Stabilin-1
Q9UKR5	-3.1579447	-4.2295370	-3.6937409	-1.0715922	2	8.494780	14.040495	0.0020276	0.0280276	Probable ergosterol biosynthetic protein 28
P13671	-1.1945588	-1.5206835	-1.3576211	-0.3261247	2	9.367147	12.786687	0.0021004	0.0282991	Complement component C6
Q99983	-2.3783961	-3.5274028	-2.9528995	-1.1490067	2	6.896719	17.159000	0.0021021	0.0282991	Osteomodulin
Q9HAV4	-2.4188578	-1.2527685	-1.8358132	1.1660893	2	7.617284	15.409738	0.0021025	0.0282991	Exportin-5
P01042	-2.2103015	-1.7555082	-1.9829048	0.4547933	2	7.253167	16.183361	0.0021174	0.0282991	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q9UJC5	-1.1209072	-1.3078139	-1.2143605	-0.1869067	2	9.327075	12.753884	0.0021439	0.0282991	SH3 domain-binding glutamic acid-rich-like protein 2
Q8NAT1	-1.3792038	-0.2825817	-0.8308927	1.0966221	2	9.307624	12.762050	0.0021515	0.0282991	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Q8WWQ0	-1.6224614	-1.0667946	-1.3446280	0.5556668	2	9.367147	12.683457	0.0021595	0.0282991	PH-interacting protein
Q96KC8	0.8974380	-2.4809443	-0.7917532	-3.3783824	2	8.255005	14.118579	0.0021666	0.0282991	DnaJ homolog subfamily C member 1
P02461	-3.6062939	-2.2605257	-2.9334098	1.3457682	2	8.363561	13.939036	0.0021726	0.0282991	Collagen alpha-1(III) chain
P45877	-1.2442932	-0.7313621	-0.9878277	0.5129311	2	9.367147	12.627015	0.0021927	0.0283790	Peptidyl-prolyl cis-trans isomerase C
P06727	-1.3683135	-0.7770234	-1.0726685	0.5912901	2	8.787743	13.278329	0.0022088	0.0284067	Apolipoprotein A-IV
Q9GZY4	-3.1557642	-0.0786773	-1.6172207	3.0770868	2	7.722737	14.892060	0.0022376	0.0285968	Cytochrome c oxidase assembly factor 1 homolog
Q9HAT2	1.3130752	1.8853962	1.5992357	0.5723210	2	9.218017	12.687258	0.0022534	0.0286183	Sialate O-acetylesterase
Q8TDB4	-1.8263115	-2.8499059	-2.3381087	-1.0235944	2	6.232826	18.690854	0.0023270	0.0293695	Protein MGARP
Q96H79	-3.2031583	-1.2709211	-2.2370397	1.9322371	2	6.147712	18.731235	0.0024240	0.0304049	Zinc finger CCCH-type antiviral protein 1-like
O15061	-0.4973971	-1.7109696	-1.1041834	-1.2135725	2	9.367147	12.220851	0.0024506	0.0304425	Synemin
P20774	-2.0543338	-1.8560527	-1.9551933	0.1982811	2	8.016847	13.927311	0.0024634	0.0304425	Mimecan
P01034	-1.6978634	-1.2374722	-1.4676678	0.4603912	2	8.805921	12.809271	0.0024720	0.0304425	Cystatin-C
Q16082	-1.2693948	-1.2565178	-1.2629563	0.0128770	2	9.006163	12.357944	0.0026185	0.0320527	Heat shock protein beta-2
Q96C86	-1.4762676	-0.2295477	-0.8529077	1.2467199	2	9.095986	12.199814	0.0026620	0.0323605	m7GpppX diphosphatase
P56539	-2.0161968	0.7435971	-0.6362998	2.7597940	2	8.545845	12.819163	0.0026755	0.0323605	Caveolin-3
Q14314	-1.7447968	-2.0661842	-1.9054905	-0.3213874	2	9.364182	11.845865	0.0027243	0.0327555	Fibroleukin
Q9Y2Z0	-1.7414076	1.2315281	-0.2549398	2.9729357	2	9.367147	11.817017	0.0027444	0.0328038	Suppressor of G2 allele of SKP1 homolog
P34932	-1.1578310	-0.6145415	-0.8861862	0.5432895	2	9.238541	11.920639	0.0027613	0.0328124	Heat shock 70 kDa protein 4
P02790	-1.1944607	-1.4349203	-1.3146905	-0.2404596	2	9.353505	11.781674	0.0027824	0.0328710	Hemopexin
Q96FN9	-0.8407260	-2.7124894	-1.7766077	-1.8717634	2	8.367147	12.791907	0.0028526	0.0333484	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
Q86VP6	-1.0994875	-1.6017144	-1.3506010	-0.5022269	2	8.499745	12.563857	0.0028947	0.0333484	Cullin-associated NEDD8-dissociated protein 1
P28300	-1.2420615	-1.6868195	-1.4644405	-0.4447581	2	7.771987	13.564653	0.0029183	0.0333484	Protein-lysine 6-oxidase
Q6UWS5	0.9069951	1.7988581	1.3529266	0.8918630	2	7.238821	14.533211	0.0029196	0.0333484	Protein PET117 homolog, mitochondrial
P62857	-0.6357057	-2.0745313	-1.3551185	-1.4388256	2	7.660192	13.748283	0.0029198	0.0333484	40S ribosomal protein S28
Q86VU5	1.5583619	1.2103632	1.3843626	-0.3479987	2	9.367147	11.598467	0.0029213	0.0333484	Catechol O-methyltransferase domain-containing protein 1
P50479	-1.8528375	-2.3116218	-2.0822296	-0.4587843	2	8.138814	12.928860	0.0029745	0.0337663	PDZ and LIM domain protein 4
Q04760	0.5374689	2.2543279	1.3958984	1.7168590	2	8.729877	12.130653	0.0030181	0.0340706	Lactoylglutathione lyase
P24311	1.7937075	0.4175563	1.1056319	-1.3761511	2	9.367147	11.344780	0.0031442	0.0350267	Cytochrome c oxidase subunit 7B, mitochondrial
Q15126	-1.0229671	-0.9691010	-0.9960340	0.0538661	2	9.367147	11.338442	0.0031500	0.0350267	Phosphomevalonate kinase
O95183	-1.3882526	-1.5142753	-1.4512639	-0.1260227	2	9.367147	11.292572	0.0031926	0.0350267	Vesicle-associated membrane protein 5
O60262	-1.5577722	-0.9540496	-1.2559109	0.6037226	2	8.646805	12.010275	0.0031936	0.0350267	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
Q9NRX4	1.2872581	1.5228435	1.4050508	0.2355855	2	9.218297	11.425046	0.0031951	0.0350267	14 kDa phosphohistidine phosphatase
P50552	-1.5288544	-0.3179222	-0.9233883	1.2109322	2	8.983622	11.639014	0.0032062	0.0350267	Vasodilator-stimulated phosphoprotein
O43143	-0.9916403	-0.7663048	-0.8789725	0.2253355	2	9.367147	11.205569	0.0032753	0.0355908	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
Q9UKX3	2.1517579	1.3923160	1.7720370	-0.7594419	2	9.185210	11.268427	0.0033723	0.0364497	Myosin-13
O43175	-2.0611208	-2.0582864	-2.0597036	0.0028343	2	9.168272	11.225282	0.0034301	0.0366874	D-3-phosphoglycerate dehydrogenase
P13667	-1.1598725	-1.0308001	-1.0953363	0.1290724	2	9.119006	11.270116	0.0034304	0.0366874	Protein disulfide-isomerase A4
P09619	-1.6085799	-0.8696596	-1.2391198	0.7389204	2	9.173401	11.188261	0.0034624	0.0368360	Platelet-derived growth factor receptor beta
Q15582	-2.0582495	-2.4708003	-2.2645249	-0.4125507	2	8.014872	12.402480	0.0035196	0.0372487	Transforming growth factor-beta-induced protein ig-h3
P46063	-1.3496984	-0.1913299	-0.7705141	1.1583685	2	9.129952	11.127049	0.0035651	0.0375354	ATP-dependent DNA helicase Q1
Q04721	1.5358466	0.7608000	1.1483233	-0.7750466	2	9.160307	10.974791	0.0036982	0.0386819	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
P82663	-0.7353102	-1.9445156	-1.3399129	-1.2092054	2	9.319706	10.825808	0.0037121	0.0386819	28S ribosomal protein S25, mitochondrial
Q9H1E5	-1.3852786	-0.6281435	-1.0067111	0.7571351	2	9.367147	10.743678	0.0037606	0.0387923	Thioredoxin-related transmembrane protein 4
P15924	1.2648885	0.5884207	0.9266546	-0.6764679	2	9.330534	10.773533	0.0037609	0.0387923	Desmoplakin
Q562R1	1.2875697	-1.9659870	-0.3392087	-3.2535567	2	9.297198	10.730636	0.0038418	0.0391158	Beta-actin-like protein 2
P26447	-1.8372154	-1.1609328	-1.4990741	0.6762826	2	8.705342	11.261795	0.0038482	0.0391158	Protein S100-A4
P46940	-1.2282390	-0.9929352	-1.1105871	0.2353038	2	9.186608	10.816277	0.0038500	0.0391158	Ras GTPase-activating-like protein IQGAP1
P00747	-0.7031792	-0.9445552	-0.8238672	-0.2413759	2	9.352906	10.639404	0.0038956	0.0393825	Plasminogen;Plasmin heavy chain A;Activation peptide;Angiostatin;Plasmin heavy chain A, short form;Plasmin light chain B
Q9BXR6	-2.3571850	-0.3244535	-1.3408193	2.0327315	2	9.364182	10.554297	0.0039875	0.0401117	Complement factor H-related protein 5
Q96CS3	-1.2719044	-1.0301135	-1.1510089	0.2417910	2	9.038275	10.795949	0.0040232	0.0402713	FAS-associated factor 2
Q8TDB6	-1.7610737	-0.2028869	-0.9819803	1.5581868	2	9.048834	10.681120	0.0041512	0.0413488	E3 ubiquitin-protein ligase DTX3L
Q07507	-0.8894252	-1.6196169	-1.2545210	-0.7301918	2	7.875411	11.880107	0.0041880	0.0414825	Dermatopontin
P61925	0.7515090	2.0311172	1.3913131	1.2796082	2	7.493224	12.391879	0.0042054	0.0414825	cAMP-dependent protein kinase inhibitor alpha
P54577	-1.3002728	-0.7367269	-1.0184999	0.5635459	2	8.963466	10.685435	0.0042375	0.0415970	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
O95445	-2.7585957	-2.3010898	-2.5298428	0.4575059	2	9.048550	10.561843	0.0043020	0.0417210	Apolipoprotein M
Q96JB2	-1.5601697	-2.5424131	-2.0512914	-0.9822435	2	8.367147	11.190372	0.0043180	0.0417210	Conserved oligomeric Golgi complex subunit 3
Q9Y5U8	-4.0913780	-0.8687357	-2.4800568	3.2226422	2	9.266368	10.368879	0.0043233	0.0417210	Mitochondrial pyruvate carrier 1
Q9UBI9	-2.9866384	-0.8834562	-1.9350473	2.1031822	2	7.178007	12.733697	0.0043560	0.0417210	Headcase protein homolog
P01019	-1.0448644	-1.0030802	-1.0239723	0.0417842	2	9.074108	10.469086	0.0043956	0.0417210	Angiotensinogen;Angiotensin-1;Angiotensin-2;Angiotensin-3;Angiotensin-4;Angiotensin 1-9;Angiotensin 1-7;Angiotensin 1-5;Angiotensin 1-4
Q9BXV9	1.6081180	1.2779850	1.4430515	-0.3301330	2	9.236097	10.319448	0.0044221	0.0417210	Uncharacterized protein C14orf142
P05455	-1.2004499	-0.5119574	-0.8562036	0.6884925	2	9.117952	10.373906	0.0044758	0.0417210	Lupus La protein
P01303	-0.6259708	-2.1513743	-1.3886725	-1.5254035	2	8.937212	10.523180	0.0044765	0.0417210	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
Q08945	-2.0204841	-0.7318160	-1.3761500	1.2886681	2	8.367147	11.057199	0.0044781	0.0417210	FACT complex subunit SSRP1
P03950	-2.2030636	-1.3551859	-1.7791248	0.8478778	2	8.151933	11.285719	0.0044812	0.0417210	Angiogenin
P27658	-1.5140155	-1.7127250	-1.6133702	-0.1987096	2	9.367147	10.166754	0.0044956	0.0417210	Collagen alpha-1(VIII) chain;Vastatin
Q8N5M1	-1.9899041	-0.5768127	-1.2833584	1.4130914	2	9.069735	10.384305	0.0045150	0.0417210	ATP synthase mitochondrial F1 complex assembly factor 2
O15111	-1.9484725	0.1796463	-0.8844131	2.1281188	2	6.903146	13.036750	0.0045272	0.0417210	Inhibitor of nuclear factor kappa-B kinase subunit alpha
P14555	-4.6109150	-1.7124375	-3.1616763	2.8984775	2	6.863351	13.099918	0.0045376	0.0417210	Phospholipase A2, membrane associated
P01611	-0.4287012	-2.2134812	-1.3210912	-1.7847800	2	9.367147	10.086482	0.0046112	0.0422067	Ig kappa chain V-I region Wes
P08582	-1.6911943	0.5093349	-0.5909297	2.2005292	2	9.341606	10.087588	0.0046371	0.0422536	Melanotransferrin
P02748	-1.3347023	-1.1111268	-1.2229145	0.2235756	2	8.859765	10.452411	0.0046629	0.0422958	Complement component C9;Complement component C9a;Complement component C9b
Q7Z3T8	-1.6269924	-1.1222772	-1.3746348	0.5047152	2	8.532932	10.727681	0.0046896	0.0422958	Zinc finger FYVE domain-containing protein 16
P83916	-1.9250014	-1.2862578	-1.6056296	0.6387436	2	6.367147	13.956675	0.0047042	0.0422958	Chromobox protein homolog 1
O95486	-1.7001274	-1.0636851	-1.3819063	0.6364423	2	9.024990	10.253966	0.0047500	0.0423505	Protein transport protein Sec24A
P80723	-1.6306847	-1.3908810	-1.5107829	0.2398038	2	7.974199	11.264618	0.0047519	0.0423505	Brain acid soluble protein 1
Q9UQR1	-1.4862974	-2.0586846	-1.7724910	-0.5723872	2	7.180587	12.311255	0.0047814	0.0424275	Zinc finger protein 148
P04350	-0.5000235	-2.8614317	-1.6807276	-2.3614082	2	6.939826	12.637041	0.0048599	0.0429361	Tubulin beta-4A chain
Q9BSD7	-0.0545512	2.9932195	1.4693342	3.0477707	2	7.153722	12.201816	0.0049484	0.0435291	Cancer-related nucleoside-triphosphatase
Q6ZSY5	-1.6890696	0.3183479	-0.6853608	2.0074175	2	9.182684	9.952141	0.0050232	0.0439966	Protein phosphatase 1 regulatory subunit 3F
P52907	-0.6341583	-1.0705881	-0.8523732	-0.4364298	2	9.367147	9.774837	0.0050955	0.0443094	F-actin-capping protein subunit alpha-1
Q9UL26	-1.3946303	7.7630062	3.1841879	9.1576365	2	8.821706	10.183942	0.0051026	0.0443094	Ras-related protein Rab-22A
P00352	-1.1750832	-1.0942191	-1.1346512	0.0808640	2	8.198138	10.686642	0.0052021	0.0449237	Retinal dehydrogenase 1
O75348	-1.8591253	-0.7192282	-1.2891767	1.1398970	2	9.367147	9.701979	0.0052175	0.0449237	V-type proton ATPase subunit G 1
P62328	-1.0872671	-1.6037620	-1.3455146	-0.5164948	2	7.466159	11.440723	0.0053266	0.0456697	Thymosin beta-4;Hematopoietic system regulatory peptide
P19447	-1.4619429	-1.7139667	-1.5879548	-0.2520238	2	7.367147	11.517190	0.0054002	0.0460309	TFIIH basal transcription factor complex helicase XPB subunit
Q9UBV8	-1.1592741	-1.1168518	-1.1380629	0.0424223	2	8.904086	9.924224	0.0054141	0.0460309	Peflin
P50991	-1.7929240	-1.2273248	-1.5101244	0.5655992	2	8.411032	10.300768	0.0054770	0.0463715	T-complex protein 1 subunit delta
Q13636	-3.2633858	-0.6868078	-1.9750968	2.5765779	2	6.180434	13.451608	0.0056038	0.0468969	Ras-related protein Rab-31
P07384	-1.1052065	-0.6231149	-0.8641607	0.4820916	2	9.248204	9.558664	0.0056143	0.0468969	Calpain-1 catalytic subunit
O75746	-1.5795706	0.3197994	-0.6298856	1.8993700	2	8.599528	10.036896	0.0056391	0.0468969	Calcium-binding mitochondrial carrier protein Aralar1
O15118	-1.6380093	-2.6115739	-2.1247916	-0.9735646	2	6.367147	13.005900	0.0056414	0.0468969	Niemann-Pick C1 protein
P07360	-0.3661706	-1.5355448	-0.9508577	-1.1693742	2	8.705608	9.940378	0.0056544	0.0468969	Complement component C8 gamma chain
Q9Y287	-1.9272432	-1.2939440	-1.6105936	0.6332992	2	9.304864	9.475995	0.0056964	0.0470534	Integral membrane protein 2B;BRI2, membrane form;BRI2 intracellular domain;BRI2C, soluble form;Bri23 peptide
O75489	1.0108281	1.0219465	1.0163873	0.0111184	2	9.367147	9.393332	0.0057754	0.0473406	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Q9NS69	-1.0528628	-1.1166761	-1.0847694	-0.0638134	2	8.742188	9.840562	0.0057778	0.0473406	Mitochondrial import receptor subunit TOM22 homolog
Q96CX2	-0.8396635	-0.9694391	-0.9045513	-0.1297756	2	9.288020	9.388436	0.0058852	0.0480268	BTB/POZ domain-containing protein KCTD12
Q96MM6	0.4030247	3.2093435	1.8061841	2.8063188	2	6.690985	12.123920	0.0059594	0.0483222	Heat shock 70 kDa protein 12B
Q6P1N0	-1.7290768	-1.5725334	-1.6508051	0.1565434	2	6.929225	11.714123	0.0059865	0.0483222	Coiled-coil and C2 domain-containing protein 1A
Q8N142	0.8908837	1.2627344	1.0768090	0.3718507	2	9.226437	9.370480	0.0060005	0.0483222	Adenylosuccinate synthetase isozyme 1
Q6IC98	-1.1710653	-0.6404079	-0.9057366	0.5306575	2	8.602633	9.819994	0.0060165	0.0483222	GRAM domain-containing protein 4
Q9UKS6	1.4372286	0.5392727	0.9882506	-0.8979559	2	8.938698	9.538129	0.0060630	0.0483630	Protein kinase C and casein kinase substrate in neurons protein 3
Q9NS86	-1.0081432	-0.9839540	-0.9960486	0.0241892	2	9.071255	9.441104	0.0060692	0.0483630	LanC-like protein 2
Q96GK7	-1.0663942	-1.4451082	-1.2557512	-0.3787140	2	7.857234	10.423090	0.0061590	0.0488869	Fumarylacetoacetate hydrolase domain-containing protein 2A
Q9UK22	-1.8807802	-0.9140754	-1.3974278	0.9667048	2	6.358956	12.504808	0.0062557	0.0494614	F-box only protein 2
Q07065	-0.7557868	-1.1419378	-0.9488623	-0.3861510	2	8.906519	9.450544	0.0062815	0.0494726	Cytoskeleton-associated protein 4
Q9BYN0	-1.2919699	-1.2682387	-1.2801043	0.0237312	2	9.118184	9.285764	0.0063190	0.0495761	Sulfiredoxin-1
Q14118	-0.8994159	-0.7980566	-0.8487363	0.1013592	2	8.728528	9.526325	0.0063915	0.0499524	Dystroglycan;Alpha-dystroglycan;Beta-dystroglycan

5.3.3 Confirmation stage

library(stageR)

## 
## Attaching package: 'stageR'

## The following object is masked from 'package:methods':
## 
##     getMethod

pAll <- sapply(
  c("omnibusTest",
    "tissueV",
    "tissueV + locationR:tissueV",
    "tissueV + 0.5 * locationR:tissueV",
    "locationR:tissueV"),
    function(name,assay)
      pull(rowData(assay)[,name],"pval"),
  assay = pe[["proteinRobust"]])
rownames(pAll) <- rownames(pe[["proteinRobust"]])

stageWiseAnalysis <- stageR(pAll[,1], pAll[,-1])
stageWiseAnalysis <- stageWiseAdjustment(stageWiseAnalysis, method = "holm", alpha = 0.05, allowNA = TRUE)

## Removing 1261 features with NA screening hypothesis p-values.

rowData(pe[["proteinRobust"]])$stageWiseAnalysis <- data.frame(pAll)
rowData(pe[["proteinRobust"]])$stageWiseAnalysis[] <- NA
rowData(pe[["proteinRobust"]])$stageWiseAnalysis[getPScreen(stageWiseAnalysis) %>% is.na %>% `!`,] <- getAdjustedPValues(stageWiseAnalysis, onlySignificantGenes=FALSE, order=FALSE)

## The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.

sigNamesStageWise <- apply(rowData(pe[["proteinRobust"]])$stageWiseAnalysis, 2, function(x) (x < 0.05) %>% which %>% names)

sapply(sigNamesStageWise,length)

##                       omnibusTest                           tissueV 
##                               260                               130 
##       tissueV...locationR.tissueV tissueV...0.5...locationR.tissueV 
##                                97                               216 
##                 locationR.tissueV 
##                                13

for (i in 1:length(sigNamesStageWise))
heatmap(assay(pe[["proteinRobust"]])[sigNamesStageWise[[i]], ], main=names(sigNamesStageWise)[i])

5.4 Confirmation improved

Instead of the Holm correction, we can use a better correction for this specific design in the confirmation stage. If we pass the screening stage we know that at least one null hypothesis related to the contrasts is false. If this is not the case we have made an false positive conclusion, but the multiple testing correction in the screening stage already accounts for that.

In the confirmation stage we have to correct for the maximum number of hypotheses that we can falsely reject. The omnibus hypothesis test essentially tests the overall null hypothesis that the log2 protein abundance is on average equal between atrium and ventriculum both in the left and right heart region. This involves testing simultaneously two model parameters: the main effect for ventriculum and the ventriculum:location interaction. All our hypotheses are based on these two model parameters, so the tests are not independent. The following configurations can occur: - None of the model parameters differ from zero, in which we can falsely reject all hypotheses. However, we already corrected for that in the screening stage! - If only the main ventriculum effect differs from zero, we know that the average log2 fold change between atrium and ventriculum left, right and overall differ from zero. So we falsely reject at most one null hypothesis, i.e. the interaction. - If only interaction differs from zero, only the null hypothesis related to log2 fold change in the left heart region can be falsely rejected. - If both the main effect and the interaction differ from zero it is possible that - the interaction is as large in magnitude as the main effect but opposite in sign. This would mean that the log2 fold change in the right heart region is zero, which we can falsely reject. - the interaction effect is twice as large in magnitude as the main effect but opposite in sign. This would mean that the log2 fold change in left and right side are equal in size but opposite in sign, implying that contrast that averages over the average log2 fold changes left and right would be zeor, which we could falsely reject - all effects are true.

Hence, as soon as we enter the confirmation stage that we can at maximum make one false rejection so for this design and for our hypotheses of interest we do not have to correct for multiple testing in the second stage because we only have to account for the fact that we can at most make one false rejection.

So we can set the method="none"

stageWiseAnalysis <- stageWiseAdjustment(stageWiseAnalysis, method = "none", alpha = 0.05, allowNA = TRUE)

## Removing 1261 features with NA screening hypothesis p-values.

rowData(pe[["proteinRobust"]])$stageWiseAnalysis <- data.frame(pAll)
rowData(pe[["proteinRobust"]])$stageWiseAnalysis[] <- NA
rowData(pe[["proteinRobust"]])$stageWiseAnalysis[getPScreen(stageWiseAnalysis) %>% is.na %>% `!`,] <- getAdjustedPValues(stageWiseAnalysis, onlySignificantGenes=FALSE, order=FALSE)

## The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.

sigNamesStageWise <- apply(rowData(pe[["proteinRobust"]])$stageWiseAnalysis, 2, function(x) (x < 0.05) %>% which %>% names)

sapply(sigNamesStageWise,length)

##                       omnibusTest                           tissueV 
##                               260                               180 
##       tissueV...locationR.tissueV tissueV...0.5...locationR.tissueV 
##                               144                               246 
##                 locationR.tissueV 
##                                21

for (i in 1:length(sigNamesStageWise))
heatmap(assay(pe[["proteinRobust"]])[sigNamesStageWise[[i]], ], main=names(sigNamesStageWise)[i])

Note, that - our more relaxed FDR correction enables us to reject more null hypotheses in the second stage. - we can recover 21 proteins with significant interactions.

It is also very important to realise that setting the method to correct for multiple testing in the second stage at method = none is only correct for very specific designs and research hypotheses that are assessed. For most analyses we suggest to use the Holm method, which always we provide correct results.