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	0.4374889	9.368515	18.212924	0.0000000	0.0000254	Myosin light chain 3
P12883	4.6698827	0.3716767	9.183035	12.564369	0.0000004	0.0004375	Myosin-7
P10916	6.9261087	0.5291437	7.368515	13.089278	0.0000023	0.0015481	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q6UWY5	-3.2536428	0.3829023	9.114628	-8.497319	0.0000126	0.0046717	Olfactomedin-like protein 1
O75368	-2.2715945	0.2715643	9.290627	-8.364851	0.0000127	0.0046717	SH3 domain-binding glutamic acid-rich-like protein
P46821	-2.1668803	0.2632989	9.368515	-8.229734	0.0000138	0.0046717	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
O95865	-2.1732192	0.2826515	9.368515	-7.688688	0.0000242	0.0065429	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q8N474	-3.3090235	0.3804612	7.898848	-8.697400	0.0000258	0.0065429	Secreted frizzled-related protein 1
Q9ULL5-3	-3.4165405	0.3999070	7.847494	-8.543337	0.0000305	0.0068822	Proline-rich protein 12
P14854	2.4019126	0.3058151	8.432836	7.854135	0.0000371	0.0069604	Cytochrome c oxidase subunit 6B1
P21810	-3.2145420	0.4216870	8.758163	-7.623053	0.0000378	0.0069604	Biglycan
O94875-10	2.3744000	0.3186369	8.906280	7.451743	0.0000411	0.0069604	Sorbin and SH3 domain-containing protein 2
P05546	-1.9318824	0.2700130	9.273028	-7.154775	0.0000458	0.0071552	Heparin cofactor 2
P29622	-2.1134793	0.3013699	9.368515	-7.012908	0.0000510	0.0073991	Kallistatin
Q16647	-2.7991521	0.3962545	9.029611	-7.064026	0.0000580	0.0078539	Prostacyclin synthase
P02452	-2.9630153	0.3999276	8.293636	-7.408880	0.0000626	0.0079564	Collagen alpha-1(I) chain
P51884	-2.1343314	0.3161009	9.158739	-6.752058	0.0000768	0.0091792	Lumican
Q8TBQ9	-2.8189960	0.4060776	8.624259	-6.942013	0.0000831	0.0093820	Protein kish-A
P07451	-1.8489373	0.2896550	9.368515	-6.383241	0.0001070	0.0096464	Carbonic anhydrase 3
P36955	-2.3377901	0.3356710	8.144923	-6.964528	0.0001071	0.0096464	Pigment epithelium-derived factor
P00325	-2.1119462	0.3236463	8.985368	-6.525476	0.0001090	0.0096464	Alcohol dehydrogenase 1B
Q9UBG0	-2.5547510	0.3974794	9.173764	-6.427380	0.0001114	0.0096464	C-type mannose receptor 2
P24844	-2.4962161	0.3930243	9.313301	-6.351303	0.0001142	0.0096464	Myosin regulatory light polypeptide 9
P23083	-4.2325442	0.5732163	7.368515	-7.383852	0.0001175	0.0096464	Ig heavy chain V-I region V35
P51888	-3.0081810	0.4005142	7.160706	-7.510798	0.0001214	0.0096464	Prolargin
Q15113	-2.7424988	0.4328085	9.187189	-6.336518	0.0001234	0.0096464	Procollagen C-endopeptidase enhancer 1
Q53GQ0	-2.4232423	0.3906302	9.358937	-6.203418	0.0001341	0.0098194	Very-long-chain 3-oxoacyl-CoA reductase
Q06828	-4.2030186	0.6622251	8.970372	-6.346813	0.0001353	0.0098194	Fibromodulin
P13533	-4.0404076	0.6482168	9.099741	-6.233112	0.0001457	0.0100599	Myosin-6
P35442	-2.3010500	0.3521288	8.368515	-6.534683	0.0001485	0.0100599	Thrombospondin-2
P08294	-2.7503241	0.4255264	7.962984	-6.463345	0.0001995	0.0129987	Extracellular superoxide dismutase [Cu-Zn]
Q96LL9	-2.4127080	0.3982253	8.758485	-6.058651	0.0002105	0.0129987	DnaJ homolog subfamily C member 30
P18428	-1.9996058	0.3386007	9.140026	-5.905498	0.0002141	0.0129987	Lipopolysaccharide-binding protein
P36021	-3.1085951	0.5037977	8.368515	-6.170324	0.0002227	0.0129987	Monocarboxylate transporter 8
Q9UL18	-2.6225313	0.4093767	7.861683	-6.406156	0.0002239	0.0129987	Protein argonaute-1
Q92508	4.0552373	0.5571260	6.368515	7.278852	0.0002599	0.0145383	Piezo-type mechanosensitive ion channel component 1
P46060	-1.9620904	0.3259590	8.368515	-6.019440	0.0002647	0.0145383	Ran GTPase-activating protein 1
P02743	-2.1700557	0.3848202	9.368515	-5.639142	0.0002744	0.0146745	Serum amyloid P-component;Serum amyloid P-component(1-203)
Q14764	-1.6267934	0.2899230	9.368515	-5.611122	0.0002847	0.0148018	Major vault protein
Q9UGT4	-2.3006162	0.4078692	9.193191	-5.640573	0.0002936	0.0148018	Sushi domain-containing protein 2
P05997	-3.0856148	0.5406155	8.941541	-5.707596	0.0002987	0.0148018	Collagen alpha-2(V) chain
Q8WWA0	-5.8725166	0.9874403	8.104172	-5.947211	0.0003262	0.0149352	Intelectin-1
O43677	-2.7199107	0.4714061	8.431964	-5.769782	0.0003446	0.0149352	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q9P2B2	-2.0393915	0.3730159	9.368515	-5.467304	0.0003447	0.0149352	Prostaglandin F2 receptor negative regulator
O60760	-3.5990151	0.6214516	8.368515	-5.791304	0.0003456	0.0149352	Hematopoietic prostaglandin D synthase
Q9UBB5	2.7451793	0.3964212	6.368515	6.924906	0.0003459	0.0149352	Methyl-CpG-binding domain protein 2
Q9BW30	-2.7245919	0.4890210	9.000584	-5.571523	0.0003466	0.0149352	Tubulin polymerization-promoting protein family member 3
P40261	-2.3445730	0.4269444	9.222067	-5.491518	0.0003528	0.0149352	Nicotinamide N-methyltransferase
P00748	-1.9914680	0.3694913	9.104470	-5.389757	0.0004219	0.0171336	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q9NZ01	-2.4109216	0.4362074	8.634144	-5.527007	0.0004252	0.0171336	Very-long-chain enoyl-CoA reductase
O14967	-2.3785961	0.4289896	8.528665	-5.544647	0.0004345	0.0171336	Calmegin
Q92736-2	-3.3064395	0.6040506	8.714858	-5.473779	0.0004401	0.0171336	Ryanodine receptor 2
P12110	-1.9881397	0.3531159	8.170387	-5.630275	0.0004567	0.0171336	Collagen alpha-2(VI) chain
Q07954	-1.6573532	0.3151713	9.368515	-5.258579	0.0004573	0.0171336	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	0.7667780	8.368515	-5.546156	0.0004638	0.0171336	Potassium channel subfamily K member 1
O95980	-2.5277905	0.4553842	8.147873	-5.550896	0.0005067	0.0183856	Reversion-inducing cysteine-rich protein with Kazal motifs
P31994-2	-1.5795166	0.3015180	9.070422	-5.238548	0.0005224	0.0186215	Low affinity immunoglobulin gamma Fc region receptor II-b
O00264	-1.9731043	0.3784635	9.045535	-5.213459	0.0005450	0.0190953	Membrane-associated progesterone receptor component 1
Q8TBP6	-1.9233155	0.3698169	8.980202	-5.200723	0.0005675	0.0193967	Solute carrier family 25 member 40
Q14195-2	-2.5380012	0.4959159	9.231543	-5.117806	0.0005816	0.0193967	Dihydropyrimidinase-related protein 3
Q8WZA9	-1.4960398	0.2916303	9.179407	-5.129918	0.0005823	0.0193967	Immunity-related GTPase family Q protein
Q9BXN1	-2.6634064	0.5179868	8.960478	-5.141842	0.0006183	0.0202651	Asporin
O43464	-1.9028432	0.3752066	9.114853	-5.071455	0.0006448	0.0207572	Serine protease HTRA2, mitochondrial
P01699	-4.3035389	0.6883933	6.250045	-6.251570	0.0006632	0.0207572	Ig lambda chain V-I region VOR
P41240	-1.5466953	0.3045232	8.998465	-5.079072	0.0006640	0.0207572	Tyrosine-protein kinase CSK
Q9GZY4	-3.1557642	0.5785126	7.724104	-5.454961	0.0006821	0.0207572	Cytochrome c oxidase assembly factor 1 homolog
P06858	1.7891922	0.3581598	9.250634	4.995514	0.0006844	0.0207572	Lipoprotein lipase
Q8NAT1	-1.3792038	0.2787555	9.308991	-4.947719	0.0007181	0.0214576	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
P04083	-1.5201990	0.3087264	9.368515	-4.924098	0.0007286	0.0214576	Annexin A1
P02747	-2.6697776	0.4696931	6.991839	-5.684089	0.0007507	0.0217904	Complement C1q subcomponent subunit C
Q92621	-1.7036447	0.3507623	9.365549	-4.856978	0.0008023	0.0226632	Nuclear pore complex protein Nup205
Q9NY15	-2.1436460	0.4431113	9.351844	-4.837714	0.0008281	0.0226632	Stabilin-1
A6NMZ7	-2.2762344	0.4709221	9.368515	-4.833569	0.0008288	0.0226632	Collagen alpha-6(VI) chain
O14980	-1.2169774	0.2518597	9.368515	-4.831966	0.0008307	0.0226632	Exportin-1
P02775	-1.9622566	0.4071230	9.368515	-4.819813	0.0008453	0.0226632	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	0.3026715	9.097353	-4.877458	0.0008476	0.0226632	m7GpppX diphosphatase
Q92604	-2.2504519	0.4678630	9.300540	-4.810066	0.0008750	0.0229136	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
P48681	-1.3334013	0.2782133	9.365549	-4.792731	0.0008796	0.0229136	Nestin
P50552	-1.5288544	0.3231881	8.984989	-4.730540	0.0010780	0.0267434	Vasodilator-stimulated phosphoprotein
P24311	1.7937075	0.3866420	9.368515	4.639194	0.0010974	0.0267434	Cytochrome c oxidase subunit 7B, mitochondrial
Q7L4S7	-1.7124303	0.3243759	7.101207	-5.279154	0.0010976	0.0267434	Protein ARMCX6
Q9UNW9	4.0122337	0.8559118	9.090331	4.687672	0.0011095	0.0267434	RNA-binding protein Nova-2
P49207	-1.5105253	0.3206276	8.972582	-4.711151	0.0011119	0.0267434	60S ribosomal protein L34
Q8WY22	-1.8091979	0.3730521	8.368515	-4.849719	0.0011190	0.0267434	BRI3-binding protein
P46063	-1.3496984	0.2888777	9.131319	-4.672214	0.0011205	0.0267434	ATP-dependent DNA helicase Q1
P56539	-2.0161968	0.4208419	8.547212	-4.790866	0.0011398	0.0267434	Caveolin-3
Q53GG5-2	-2.9088697	0.6016365	8.357999	-4.834929	0.0011450	0.0267434	PDZ and LIM domain protein 3
Q5M9N0	-3.5146838	0.7310629	8.333797	-4.807635	0.0011967	0.0275602	Coiled-coil domain-containing protein 158
Q6SZW1	-2.6395602	0.5186975	7.368515	-5.088824	0.0012127	0.0275602	Sterile alpha and TIR motif-containing protein 1
Q9HAV4	-2.4188578	0.4846305	7.618651	-4.991138	0.0012311	0.0275602	Exportin-5
Q5NDL2	-2.2948242	0.4878301	8.665876	-4.704146	0.0012342	0.0275602	EGF domain-specific O-linked N-acetylglucosamine transferase
Q9BXR6	-2.3571850	0.5178806	9.365549	-4.551600	0.0012486	0.0275773	Complement factor H-related protein 5
Q92681	-2.1962163	0.4494647	7.880492	-4.886293	0.0012685	0.0276163	Regulatory solute carrier protein family 1 member 1
O15230	-1.4246624	0.3044130	8.637704	-4.680032	0.0012870	0.0276163	Laminin subunit alpha-5
Q8TDB6	-1.7610737	0.3837173	9.050201	-4.589509	0.0012911	0.0276163	E3 ubiquitin-protein ligase DTX3L
Q96H79	-3.2031583	0.5750970	6.149079	-5.569770	0.0013082	0.0276900	Zinc finger CCCH-type antiviral protein 1-like
P14550	-1.3982496	0.3048645	8.804116	-4.586463	0.0013931	0.0289445	Alcohol dehydrogenase [NADP(+)]
Q15274	-1.9285076	0.4005465	7.864253	-4.814691	0.0013959	0.0289445	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q9BUF5	-1.9157084	0.4272933	9.249220	-4.483357	0.0014245	0.0292392	Tubulin beta-6 chain
O15111	-1.9484725	0.3816220	6.904513	-5.105766	0.0014498	0.0293778	Inhibitor of nuclear factor kappa-B kinase subunit alpha
Q12996	-2.0094808	0.3792730	6.441996	-5.298244	0.0014664	0.0293778	Cleavage stimulation factor subunit 3
Q9Y5U8	-4.0913780	0.9180772	9.267735	-4.456464	0.0014747	0.0293778	Mitochondrial pyruvate carrier 1
P06727	-1.3683135	0.3016794	8.789110	-4.535654	0.0015028	0.0296482	Apolipoprotein A-IV
P04196	-1.9303128	0.3967844	7.454498	-4.864890	0.0015267	0.0297339	Histidine-rich glycoprotein
O75828	-1.6544202	0.3750717	9.368515	-4.410944	0.0015364	0.0297339	Carbonyl reductase [NADPH] 3
Q9UBI9	-2.9866384	0.6064805	7.179374	-4.924542	0.0015849	0.0303814	Headcase protein homolog
P01031	-1.3157564	0.2894433	8.493085	-4.545818	0.0016173	0.0305961	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q9ULC3	-1.6333020	0.3626056	8.668837	-4.504349	0.0016262	0.0305961	Ras-related protein Rab-23
Q6ZSY5	-1.6890696	0.3854953	9.184051	-4.381557	0.0016835	0.0313140	Protein phosphatase 1 regulatory subunit 3F
P45877	-1.2442932	0.2872374	9.368515	-4.331934	0.0017293	0.0313140	Peptidyl-prolyl cis-trans isomerase C
P02461	-3.6062939	0.7973543	8.364929	-4.522825	0.0017349	0.0313140	Collagen alpha-1(III) chain
P04003	-1.5009188	0.3412528	8.971202	-4.398261	0.0017381	0.0313140	C4b-binding protein alpha chain
P14555	-4.6109150	0.9304138	6.864718	-4.955768	0.0017414	0.0313140	Phospholipase A2, membrane associated
Q8N5M1	-1.9899041	0.4556449	9.071102	-4.367225	0.0017709	0.0315654	ATP synthase mitochondrial F1 complex assembly factor 2
P08582	-1.6911943	0.3933014	9.342973	-4.299996	0.0018259	0.0322623	Melanotransferrin
Q6YN16	1.5603531	0.3639389	9.368515	4.287404	0.0018492	0.0323923	Hydroxysteroid dehydrogenase-like protein 2
P34932	-1.1578310	0.2691695	9.239908	-4.301494	0.0018690	0.0324093	Heat shock 70 kDa protein 4
Q9UQ35	-1.3570787	0.3179436	9.349254	-4.268300	0.0019122	0.0324093	Serine/arginine repetitive matrix protein 2
O75746	-1.5795706	0.3588123	8.600896	-4.402220	0.0019135	0.0324093	Calcium-binding mitochondrial carrier protein Aralar1
Q13636	-3.2633858	0.6324015	6.181801	-5.160307	0.0019139	0.0324093	Ras-related protein Rab-31
Q5VIR6-4	-1.7638024	0.4128098	9.115375	-4.272675	0.0020127	0.0332574	Vacuolar protein sorting-associated protein 53 homolog
P02776	-1.7615098	0.3922079	7.977340	-4.491266	0.0020398	0.0332574	Platelet factor 4;Platelet factor 4, short form
P04004	-1.6269790	0.3756281	8.733254	-4.331356	0.0020404	0.0332574	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
Q9H1E5	-1.3852786	0.3281530	9.368515	-4.221442	0.0020432	0.0332574	Thioredoxin-related transmembrane protein 4
P04209	1.3436120	0.3156818	9.138536	4.256223	0.0020506	0.0332574	Ig lambda chain V-II region NIG-84
P01042	-2.2103015	0.4729877	7.254535	-4.673063	0.0020728	0.0332574	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q8WWQ0	-1.6224614	0.3855430	9.368515	-4.208251	0.0020846	0.0332574	PH-interacting protein
P15924	1.2648885	0.3003985	9.331901	4.210702	0.0020950	0.0332574	Desmoplakin
Q2TAA5	-1.2916274	0.3068223	9.182611	-4.209692	0.0021746	0.0341685	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
Q9BTV4	-1.8099873	0.4311412	9.159972	-4.198131	0.0022247	0.0341685	Transmembrane protein 43
P05455	-1.2004499	0.2855438	9.119319	-4.204083	0.0022268	0.0341685	Lupus La protein
Q08945	-2.0204841	0.4657252	8.368515	-4.338362	0.0022336	0.0341685	FACT complex subunit SSRP1
Q04721	1.5358466	0.3667137	9.161674	4.188135	0.0022574	0.0341685	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
Q53T59	-1.8461756	0.4183746	7.985793	-4.412734	0.0022579	0.0341685	HCLS1-binding protein 3
Q9Y6X5	-1.3875045	0.3248674	8.653249	-4.270987	0.0022726	0.0341685	Bis(5-adenosyl)-triphosphatase ENPP4
P09619	-1.6085799	0.3850664	9.174768	-4.177410	0.0022869	0.0341685	Platelet-derived growth factor receptor beta
Q5JPH6	3.5281305	0.6835346	5.777444	5.161597	0.0023421	0.0347386	Probable glutamate–tRNA ligase, mitochondrial
O60262	-1.5577722	0.3669975	8.648172	-4.244639	0.0023632	0.0347970	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
O75348	-1.8591253	0.4525309	9.368515	-4.108284	0.0024282	0.0354135	V-type proton ATPase subunit G 1
O00303	-1.4561773	0.3498528	8.999343	-4.162257	0.0024399	0.0354135	Eukaryotic translation initiation factor 3 subunit F
P01034	-1.6978634	0.4073351	8.807288	-4.168222	0.0025350	0.0365096	Cystatin-C
P49458	-2.2735269	0.5032218	7.199990	-4.517942	0.0025514	0.0365096	Signal recognition particle 9 kDa protein
P25940	-1.7454125	0.4259317	9.103774	-4.097870	0.0026210	0.0372440	Collagen alpha-3(V) chain
P62760	-1.9146688	0.4698555	9.107922	-4.075016	0.0027103	0.0382458	Visinin-like protein 1
P08311	-1.3139510	0.3211076	8.830393	-4.091933	0.0028201	0.0395203	Cathepsin G
Q9UKS6	1.4372286	0.3534229	8.940065	4.066597	0.0028534	0.0396663	Protein kinase C and casein kinase substrate in neurons protein 3
Q14019	-3.9129083	0.8342355	6.368515	-4.690412	0.0028714	0.0396663	Coactosin-like protein
P36551	-1.3202398	0.3266829	9.026924	-4.041350	0.0029048	0.0396663	Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial
O15116	-3.2231772	0.6507889	5.742785	-4.952723	0.0029099	0.0396663	U6 snRNA-associated Sm-like protein LSm1
P30405	-1.5177122	0.3806790	9.368515	-3.986855	0.0029281	0.0396663	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q9UKX3	2.1517579	0.5372810	9.186578	4.004902	0.0029622	0.0398620	Myosin-13
Q9Y2Z0	-1.7414076	0.4387308	9.368515	-3.969194	0.0030094	0.0402315	Suppressor of G2 allele of SKP1 homolog
P54577	-1.3002728	0.3236946	8.964834	-4.016975	0.0030561	0.0405880	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
P19429	2.3063639	0.5565591	8.159346	4.143970	0.0030999	0.0409030	Troponin I, cardiac muscle
P54652	-1.5932853	0.4010290	9.079911	-3.972992	0.0031835	0.0417341	Heat shock-related 70 kDa protein 2
O75475	-1.9038879	0.4838818	9.241155	-3.934613	0.0032613	0.0424809	PC4 and SFRS1-interacting protein
P25311	-1.5051007	0.3734151	8.504397	-4.030637	0.0033363	0.0431807	Zinc-alpha-2-glycoprotein
P60468	-1.4647431	0.3603660	8.223714	-4.064599	0.0034074	0.0437326	Protein transport protein Sec61 subunit beta
Q9BS26	-1.2463986	0.3202162	9.302987	-3.892366	0.0034375	0.0437326	Endoplasmic reticulum resident protein 44
Q7LBR1	-2.8413335	0.7317916	9.368515	-3.882709	0.0034435	0.0437326	Charged multivesicular body protein 1b
Q04941	-1.9356392	0.4951777	9.070341	-3.908979	0.0035171	0.0443900	Proteolipid protein 2
P03950	-2.2030636	0.5449177	8.153301	-4.042929	0.0035767	0.0448495	Angiogenin
Q1KMD3	-1.4744120	0.3778552	9.013577	-3.902055	0.0035977	0.0448495	Heterogeneous nuclear ribonucleoprotein U-like protein 2
Q13641	-2.2297004	0.5229809	7.060025	-4.263445	0.0036586	0.0452090	Trophoblast glycoprotein
P26447	-1.8372154	0.4670904	8.706709	-3.933319	0.0036710	0.0452090	Protein S100-A4
Q96PK6	-1.3089284	0.3377599	9.066841	-3.875322	0.0037058	0.0453625	RNA-binding protein 14
Q9Y3B4	-1.2603707	0.3260854	9.016576	-3.865155	0.0038037	0.0455737	Splicing factor 3B subunit 6
Q9HB40	-2.1393191	0.4806306	6.309415	-4.451067	0.0038266	0.0455737	Retinoid-inducible serine carboxypeptidase
P01024	-1.1180307	0.2906729	9.105940	-3.846354	0.0038433	0.0455737	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	0.6370632	9.293824	-3.819943	0.0038557	0.0455737	Nucleolar protein 56
P12814	-1.6827515	0.4222196	8.158010	-3.985489	0.0038743	0.0455737	Alpha-actinin-1
Q13478	-1.6083281	0.4167076	8.946264	-3.859609	0.0038930	0.0455737	Interleukin-18 receptor 1
Q86VU5	1.5583619	0.4096938	9.368515	3.803724	0.0038977	0.0455737	Catechol O-methyltransferase domain-containing protein 1
P07384	-1.1052065	0.2894856	9.249572	-3.817829	0.0039025	0.0455737	Calpain-1 catalytic subunit
P01008	-1.5692162	0.4138377	9.324724	-3.791864	0.0040049	0.0463172	Antithrombin-III
P14543	-1.4365423	0.3761434	9.101457	-3.819135	0.0040117	0.0463172	Nidogen-1
O94919	-1.1247209	0.2952221	9.132259	-3.809744	0.0040452	0.0463476	Endonuclease domain-containing 1 protein
Q9UK22	-1.8807802	0.4297683	6.360323	-4.376265	0.0040823	0.0463476	F-box only protein 2
P07357	-1.1425305	0.3015073	9.211049	-3.789396	0.0041105	0.0463476	Complement component C8 alpha chain
Q7Z3T8	-1.6269924	0.4197642	8.534300	-3.875967	0.0041539	0.0463476	Zinc finger FYVE domain-containing protein 16
O95486	-1.7001274	0.4471130	9.026357	-3.802456	0.0041791	0.0463476	Protein transport protein Sec24A
Q9BXY0	-1.9170100	0.4360325	6.228522	-4.396484	0.0041948	0.0463476	Protein MAK16 homolog
Q14011	-2.3803571	0.6080407	8.235300	-3.914799	0.0042056	0.0463476	Cold-inducible RNA-binding protein
Q9Y2D4	-2.0300937	0.5287368	8.670699	-3.839517	0.0042554	0.0463476	Exocyst complex component 6B
Q96ST3	-1.6077298	0.4246620	9.054820	-3.785905	0.0042626	0.0463476	Paired amphipathic helix protein Sin3a
O43143	-0.9916403	0.2647623	9.368515	-3.745398	0.0042734	0.0463476	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
P56199	-1.2716373	0.3308282	8.591843	-3.843800	0.0043013	0.0463476	Integrin alpha-1
Q6IC98	-1.1710653	0.3048547	8.604001	-3.841388	0.0043054	0.0463476	GRAM domain-containing protein 4
P09467	-2.0219103	0.4940462	7.221982	-4.092553	0.0043188	0.0463476	Fructose-1,6-bisphosphatase 1
P51665	-1.2958979	0.3454543	9.245677	-3.751286	0.0043337	0.0463476	26S proteasome non-ATPase regulatory subunit 7
Q9BVC6	-1.6329609	0.4374434	9.368515	-3.732965	0.0043582	0.0463662	Transmembrane protein 109
P50991	-1.7929240	0.4656130	8.412399	-3.850674	0.0044305	0.0468899	T-complex protein 1 subunit delta
Q96FJ2	1.5408850	0.4060546	8.593395	3.794773	0.0046255	0.0486997	Dynein light chain 2, cytoplasmic
P23434	1.1390966	0.3085839	9.368515	3.691367	0.0046553	0.0487609	Glycine cleavage system H protein, mitochondrial
Q8NBF2	-1.1613746	0.3146320	9.295600	-3.691216	0.0047190	0.0491747	NHL repeat-containing protein 2
P04843	-2.0344244	0.5394794	8.620081	-3.771088	0.0047653	0.0493851	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
Q53FA7	1.8348852	0.4959924	9.148525	3.699422	0.0047878	0.0493851	Quinone oxidoreductase PIG3
Q6P1N0	-1.7290768	0.4243143	6.930592	-4.074991	0.0048200	0.0494662	Coiled-coil and C2 domain-containing protein 1A
Q6P587	5.5394450	1.3284598	6.530599	4.169825	0.0048817	0.0498470	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	0.4374889	9.368515	12.580521	0.0000004	0.0007157	Myosin light chain 3
P06858	3.354674	0.3544786	9.250634	9.463685	0.0000046	0.0047172	Lipoprotein lipase
Q9ULD0	-3.575906	0.3737560	7.368515	-9.567490	0.0000205	0.0138756	2-oxoglutarate dehydrogenase-like, mitochondrial
P35442	-3.246460	0.4066033	8.368515	-7.984343	0.0000343	0.0146183	Thrombospondin-2
P02776	-2.818363	0.3421721	7.977340	-8.236685	0.0000360	0.0146183	Platelet factor 4;Platelet factor 4, short form
P21810	-2.924783	0.4081234	8.758163	-7.166417	0.0000606	0.0197041	Biglycan
O75368	-1.819326	0.2697486	9.290627	-6.744524	0.0000724	0.0197041	SH3 domain-binding glutamic acid-rich-like protein
A6NMZ7	-3.070848	0.4709221	9.368515	-6.520924	0.0000906	0.0197041	Collagen alpha-6(VI) chain
P54652	-2.726681	0.4117125	9.079911	-6.622780	0.0000928	0.0197041	Heat shock-related 70 kDa protein 2
Q6UWY5	-2.456874	0.3739474	9.114628	-6.570106	0.0000970	0.0197041	Olfactomedin-like protein 1
Q06828	-4.122091	0.6363871	8.970372	-6.477332	0.0001161	0.0198355	Fibromodulin
P05546	-1.727800	0.2722600	9.273028	-6.346141	0.0001171	0.0198355	Heparin cofactor 2
P28066	-2.176824	0.3385894	8.731150	-6.429098	0.0001384	0.0205309	Proteasome subunit alpha type-5
P29622	-1.847919	0.3013699	9.368515	-6.131733	0.0001459	0.0205309	Kallistatin
P46821	-1.606539	0.2632989	9.368515	-6.101576	0.0001516	0.0205309	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P13533	-3.888317	0.6376165	9.099741	-6.098206	0.0001717	0.0218011	Myosin-6
Q9UGT4	-2.443145	0.4143494	9.193191	-5.896340	0.0002117	0.0245530	Sushi domain-containing protein 2
P35625	-3.938312	0.6160730	7.941649	-6.392605	0.0002175	0.0245530	Metalloproteinase inhibitor 3
Q6PCB0	-2.328852	0.4034039	8.935408	-5.773003	0.0002758	0.0263496	von Willebrand factor A domain-containing protein 1
Q69YU5	3.254738	0.5557216	8.696790	5.856778	0.0002760	0.0263496	Uncharacterized protein C12orf73
Q15327	-2.203003	0.3936472	9.237782	-5.596389	0.0003055	0.0263496	Ankyrin repeat domain-containing protein 1
O43677	-2.969964	0.5063192	8.431964	-5.865793	0.0003075	0.0263496	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q14764	-1.608232	0.2899230	9.368515	-5.547100	0.0003099	0.0263496	Major vault protein
P60468	-2.438022	0.4112085	8.223714	-5.928921	0.0003147	0.0263496	Protein transport protein Sec61 subunit beta
P01031	-1.626524	0.2813575	8.493085	-5.780986	0.0003309	0.0263496	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q9P2B2	-2.035226	0.3730159	9.368515	-5.456136	0.0003499	0.0263496	Prostaglandin F2 receptor negative regulator
Q92930	-2.833666	0.4661159	7.610113	-6.079316	0.0003613	0.0263496	Ras-related protein Rab-8B
P02775	-2.205543	0.4071230	9.368515	-5.417387	0.0003686	0.0263496	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	0.4884361	7.573178	-6.059605	0.0003761	0.0263496	NADP-dependent malic enzyme
P48681	-1.491288	0.2782821	9.365549	-5.358907	0.0003993	0.0269399	Nestin
P12883	1.969100	0.3655019	9.183035	5.387387	0.0004110	0.0269399	Myosin-7
P11586	2.013301	0.3518834	7.997030	5.721501	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	0.4483501	9.038732	-5.178409	0.0005727	0.0337260	Glutathione S-transferase theta-1
Q9BZH6	3.442805	0.6418413	8.321746	5.363951	0.0005911	0.0337260	WD repeat-containing protein 11
Q9H1K0	-2.237374	0.3907006	7.368515	-5.726570	0.0005948	0.0337260	Rabenosyn-5
Q9UHG2	-3.175806	0.6109007	8.845467	-5.198562	0.0005975	0.0337260	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
P00748	-1.915326	0.3787423	9.104470	-5.057070	0.0006599	0.0359543	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q5NDL2	-2.708130	0.5255026	8.665876	-5.153409	0.0006768	0.0359543	EGF domain-specific O-linked N-acetylglucosamine transferase
O00180	-4.621308	0.8853990	8.368515	-5.219464	0.0006951	0.0359543	Potassium channel subfamily K member 1
Q00G26	1.964123	0.3594514	7.551962	5.464224	0.0007287	0.0359543	Perilipin-5
P23142	-2.779235	0.5081787	7.537201	-5.469011	0.0007296	0.0359543	Fibulin-1
P10916	2.921175	0.5291437	7.368515	5.520571	0.0007443	0.0359543	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q09161	2.370716	0.3866868	6.161878	6.130844	0.0007788	0.0359543	Nuclear cap-binding protein subunit 1
P18428	-1.690875	0.3454476	9.140026	-4.894737	0.0008163	0.0359543	Lipopolysaccharide-binding protein
Q9BW30	-2.326597	0.4724143	9.000584	-4.924908	0.0008189	0.0359543	Tubulin polymerization-promoting protein family member 3
P30405	-1.842938	0.3806790	9.368515	-4.841185	0.0008199	0.0359543	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q5JPH6	3.287773	0.5184787	5.777444	6.341193	0.0008342	0.0359543	Probable glutamate–tRNA ligase, mitochondrial
Q9NRG4	2.622493	0.5180776	8.368515	5.061970	0.0008493	0.0359543	N-lysine methyltransferase SMYD2
Q9BUH6	-1.485484	0.3066662	9.144447	-4.843978	0.0008752	0.0362862	Protein PAXX
P35052	-1.965366	0.3779521	7.795481	-5.200039	0.0008929	0.0362862	Glypican-1;Secreted glypican-1
O15061	-1.710970	0.3604219	9.368515	-4.747130	0.0009384	0.0373880	Synemin
P08603	-1.484314	0.3148296	9.368515	-4.714659	0.0009835	0.0384302	Complement factor H
Q96FN9	-2.712489	0.5552397	8.368515	-4.885258	0.0010680	0.0392034	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
Q8N474	-2.108536	0.4206958	7.898848	-5.012021	0.0010775	0.0392034	Secreted frizzled-related protein 1
Q04760	2.254328	0.4708253	8.731244	4.788035	0.0010779	0.0392034	Lactoylglutathione lyase
Q96KC8	-2.480944	0.5057664	8.256372	-4.905316	0.0010820	0.0392034	DnaJ homolog subfamily C member 1
P04004	-1.908509	0.3998635	8.733254	-4.772902	0.0010997	0.0392034	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
Q99983	-3.527403	0.6600876	6.898086	-5.343840	0.0011235	0.0393616	Osteomodulin
P24298	1.991397	0.4184366	8.589351	4.759136	0.0011734	0.0404134	Alanine aminotransferase 1
P62857	-2.074531	0.4153921	7.661559	-4.994152	0.0012063	0.0408539	40S ribosomal protein S28
P23434	1.406476	0.3085839	9.368515	4.557840	0.0012362	0.0411788	Glycine cleavage system H protein, mitochondrial
P24844	-1.767461	0.3911777	9.313301	-4.518307	0.0013300	0.0435900	Myosin regulatory light polypeptide 9
P04275	-1.352764	0.2984968	8.944173	-4.531921	0.0014450	0.0453761	von Willebrand factor;von Willebrand antigen 2
Q6PI78	1.975693	0.4381010	9.040329	4.509673	0.0014519	0.0453761	Transmembrane protein 65
Q15113	-1.959899	0.4399417	9.187189	-4.454905	0.0015102	0.0453761	Procollagen C-endopeptidase enhancer 1
P01611	-2.213481	0.5019736	9.368515	-4.409557	0.0015396	0.0453761	Ig kappa chain V-I region Wes
Q86WV6	-1.310297	0.2963017	9.223994	-4.422171	0.0015692	0.0453761	Stimulator of interferon genes protein
Q6UWS5	1.798858	0.3672722	7.240188	4.897888	0.0015957	0.0453761	Protein PET117 homolog, mitochondrial
P51888	-1.838614	0.3737178	7.160706	-4.919793	0.0016056	0.0453761	Prolargin
Q9BSD7	2.993219	0.6090575	7.155089	4.914510	0.0016191	0.0453761	Cancer-related nucleoside-triphosphatase
P04350	-2.861432	0.5736880	6.941194	-4.987783	0.0016267	0.0453761	Tubulin beta-4A chain
Q7L4S7	-2.514619	0.5106906	7.101207	-4.923958	0.0016368	0.0453761	Protein ARMCX6
P08294	-1.884866	0.4043561	7.962984	-4.661402	0.0016407	0.0453761	Extracellular superoxide dismutase [Cu-Zn]
P82663	-1.944516	0.4465777	9.321073	-4.354260	0.0016925	0.0453761	28S ribosomal protein S25, mitochondrial
P50453	-1.398216	0.3163208	8.946744	-4.420249	0.0016949	0.0453761	Serpin B9
P01303	-2.151374	0.4868448	8.938580	-4.419014	0.0017017	0.0453761	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
Q9UL26	7.763006	1.7508348	8.823073	4.433888	0.0017195	0.0453761	Ras-related protein Rab-22A
Q8TDB4	-2.849906	0.5487289	6.234194	-5.193650	0.0018043	0.0463060	Protein MGARP
Q9HCB6	-2.412515	0.5438871	8.642251	-4.435691	0.0018043	0.0463060	Spondin-1
Q9Y6X5	-1.531154	0.3463868	8.653249	-4.420359	0.0018380	0.0463060	Bis(5-adenosyl)-triphosphatase ENPP4
Q15274	-2.142900	0.4681195	7.864253	-4.577678	0.0018893	0.0463060	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q6YN16	1.553070	0.3639389	9.368515	4.267391	0.0019059	0.0463060	Hydroxysteroid dehydrogenase-like protein 2
P51884	-1.386041	0.3222151	9.158739	-4.301603	0.0019072	0.0463060	Lumican
P02452	-1.816507	0.4067095	8.293636	-4.466350	0.0019142	0.0463060	Collagen alpha-1(I) chain
P61925	2.031117	0.4367868	7.494591	4.650134	0.0019552	0.0467400	cAMP-dependent protein kinase inhibitor alpha
P07360	-1.535545	0.3537800	8.706976	-4.340395	0.0020285	0.0479292	Complement component C8 gamma chain
Q96MM6	3.209344	0.6626323	6.692352	4.843324	0.0021214	0.0495483	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	0.3093513	9.368515	21.774254	0.0000000	0.0000049	Myosin light chain 3
P12883	3.3194914	0.2606411	9.183035	12.735870	0.0000004	0.0003887	Myosin-7
O75368	-2.0454601	0.1913841	9.290627	-10.687724	0.0000016	0.0007076	SH3 domain-binding glutamic acid-rich-like protein
Q6UWY5	-2.8552584	0.2676055	9.114628	-10.669655	0.0000019	0.0007076	Olfactomedin-like protein 1
P10916	4.9236420	0.3661137	7.368515	13.448397	0.0000019	0.0007076	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
P46821	-1.8867094	0.1861805	9.368515	-10.133767	0.0000024	0.0007076	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P06858	2.5719330	0.2519591	9.250634	10.207741	0.0000024	0.0007076	Lipoprotein lipase
P21810	-3.0696624	0.2931271	8.758163	-10.472121	0.0000030	0.0007653	Biglycan
P05546	-1.8298412	0.1917241	9.273028	-9.544138	0.0000042	0.0009132	Heparin cofactor 2
P35442	-2.7737551	0.2689428	8.368515	-10.313550	0.0000048	0.0009132	Thrombospondin-2
P29622	-1.9806994	0.2131007	9.368515	-9.294664	0.0000049	0.0009132	Kallistatin
Q06828	-4.1625547	0.4592196	8.970372	-9.064410	0.0000082	0.0013946	Fibromodulin
P13533	-3.9643622	0.4545529	9.099741	-8.721454	0.0000103	0.0016051	Myosin-6
Q8N474	-2.7087798	0.2821950	7.898848	-9.598963	0.0000126	0.0018228	Secreted frizzled-related protein 1
Q9UGT4	-2.3718806	0.2907072	9.193191	-8.159002	0.0000166	0.0020430	Sushi domain-containing protein 2
A6NMZ7	-2.6735410	0.3329922	9.368515	-8.028839	0.0000169	0.0020430	Collagen alpha-6(VI) chain
O95865	-1.5898713	0.1998648	9.368515	-7.954734	0.0000183	0.0020430	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q14764	-1.6175126	0.2050065	9.368515	-7.890054	0.0000196	0.0020430	Major vault protein
O94875-10	1.8826268	0.2305212	8.906280	8.166827	0.0000200	0.0020430	Sorbin and SH3 domain-containing protein 2
P02776	-2.2899367	0.2602445	7.977340	-8.799175	0.0000223	0.0020430	Platelet factor 4;Platelet factor 4, short form
Q9P2B2	-2.0373086	0.2637621	9.368515	-7.724039	0.0000233	0.0020430	Prostaglandin F2 receptor negative regulator
P51884	-1.7601864	0.2256891	9.158739	-7.799164	0.0000245	0.0020430	Lumican
P24844	-2.1318385	0.2772580	9.313301	-7.689006	0.0000250	0.0020430	Myosin regulatory light polypeptide 9
P02452	-2.3897612	0.2850308	8.293636	-8.384220	0.0000251	0.0020430	Collagen alpha-1(I) chain
Q16647	-2.1622988	0.2760261	9.029611	-7.833675	0.0000257	0.0020430	Prostacyclin synthase
O43677	-2.8449373	0.3457337	8.431964	-8.228696	0.0000261	0.0020430	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q15113	-2.3511987	0.3085741	9.187189	-7.619559	0.0000291	0.0021486	Procollagen C-endopeptidase enhancer 1
P18428	-1.8452405	0.2418572	9.140026	-7.629462	0.0000296	0.0021486	Lipopolysaccharide-binding protein
P54652	-2.1599833	0.2873754	9.079911	-7.516243	0.0000346	0.0024239	Heat shock-related 70 kDa protein 2
P51888	-2.4233975	0.2713758	7.160706	-8.930042	0.0000391	0.0024498	Prolargin
P00748	-1.9533971	0.2645607	9.104470	-7.383549	0.0000393	0.0024498	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
P02775	-2.0838997	0.2878794	9.368515	-7.238794	0.0000395	0.0024498	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	0.3399694	9.000584	-7.428887	0.0000398	0.0024498	Tubulin polymerization-promoting protein family member 3
P48681	-1.4123446	0.1967508	9.365549	-7.178341	0.0000423	0.0025310	Nestin
P14854	1.7251878	0.2271396	8.432836	7.595274	0.0000477	0.0027276	Cytochrome c oxidase subunit 6B1
P08294	-2.3175953	0.2927548	7.962984	-7.916507	0.0000483	0.0027276	Extracellular superoxide dismutase [Cu-Zn]
O00180	-4.4369891	0.5856364	8.368515	-7.576355	0.0000507	0.0027830	Potassium channel subfamily K member 1
P02743	-1.8823835	0.2721089	9.368515	-6.917757	0.0000569	0.0030401	Serum amyloid P-component;Serum amyloid P-component(1-203)
P01031	-1.4711401	0.2020912	8.493085	-7.279584	0.0000631	0.0032853	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q5NDL2	-2.5014769	0.3585147	8.665876	-6.977334	0.0000782	0.0039706	EGF domain-specific O-linked N-acetylglucosamine transferase
Q92508	3.5430878	0.3987228	6.368515	8.886092	0.0000807	0.0039988	Piezo-type mechanosensitive ion channel component 1
Q53GQ0	-1.8169289	0.2763280	9.358937	-6.575262	0.0000853	0.0040169	Very-long-chain 3-oxoacyl-CoA reductase
P05997	-2.5486728	0.3783503	8.941541	-6.736279	0.0000876	0.0040169	Collagen alpha-2(V) chain
P60468	-1.9513827	0.2743948	8.223714	-7.111587	0.0000880	0.0040169	Protein transport protein Sec61 subunit beta
P23083	-3.2601200	0.4233483	7.368515	-7.700799	0.0000890	0.0040169	Ig heavy chain V-I region V35
Q9ULL5-3	-2.3006667	0.3151373	7.847494	-7.300521	0.0000924	0.0040825	Proline-rich protein 12
Q8TBP6	-1.7084465	0.2569648	8.980202	-6.648563	0.0000949	0.0041007	Solute carrier family 25 member 40
P28066	-1.6712466	0.2477038	8.731150	-6.746955	0.0000969	0.0041007	Proteasome subunit alpha type-5
P35625	-2.9679404	0.4156910	7.941649	-7.139775	0.0001017	0.0042098	Metalloproteinase inhibitor 3
Q14195-2	-2.2534620	0.3485621	9.231543	-6.465022	0.0001036	0.0042098	Dihydropyrimidinase-related protein 3
P46060	-1.7047689	0.2489553	8.368515	-6.847691	0.0001062	0.0042304	Ran GTPase-activating protein 1
Q15327	-1.7740861	0.2767608	9.237782	-6.410179	0.0001103	0.0043092	Ankyrin repeat domain-containing protein 1
Q9ULD0	-2.0406330	0.2760371	7.368515	-7.392605	0.0001165	0.0043311	2-oxoglutarate dehydrogenase-like, mitochondrial
Q6PCB0	-1.8163629	0.2803737	8.935408	-6.478364	0.0001180	0.0043311	von Willebrand factor A domain-containing protein 1
P00325	-1.5034066	0.2330676	8.985368	-6.450516	0.0001189	0.0043311	Alcohol dehydrogenase 1B
Q69YU5	2.5059630	0.3814715	8.696790	6.569201	0.0001202	0.0043311	Uncharacterized protein C12orf73
P07451	-1.2833190	0.2048170	9.368515	-6.265686	0.0001236	0.0043311	Carbonic anhydrase 3
O14980	-1.1146843	0.1780917	9.368515	-6.259048	0.0001246	0.0043311	Exportin-1
P30405	-1.6803249	0.2691807	9.368515	-6.242368	0.0001272	0.0043311	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Q92604	-2.0782169	0.3317976	9.300540	-6.263507	0.0001279	0.0043311	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
P04004	-1.7677440	0.2743115	8.733254	-6.444294	0.0001359	0.0045119	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P36955	-1.6933164	0.2522971	8.144923	-6.711598	0.0001390	0.0045119	Pigment epithelium-derived factor
P41240	-1.3344948	0.2115827	8.998465	-6.307203	0.0001399	0.0045119	Tyrosine-protein kinase CSK
P04083	-1.3421955	0.2183025	9.368515	-6.148327	0.0001430	0.0045388	Annexin A1
P36021	-2.5034435	0.3847819	8.368515	-6.506137	0.0001532	0.0047901	Monocarboxylate transporter 8
Q6YN16	1.5567113	0.2573436	9.368515	6.049154	0.0001619	0.0049838	Hydroxysteroid dehydrogenase-like protein 2
Q8TBQ9	-1.7482778	0.2777046	8.624259	-6.295459	0.0001702	0.0051617	Protein kish-A
Q15274	-2.0357040	0.3069062	7.864253	-6.632984	0.0001767	0.0051999	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q8WWA0	-4.4529908	0.6848956	8.104172	-6.501707	0.0001774	0.0051999	Intelectin-1
Q9BXN1	-2.2858485	0.3737780	8.960478	-6.115524	0.0001791	0.0051999	Asporin
P04003	-1.4359842	0.2367789	8.971202	-6.064664	0.0001896	0.0054256	C4b-binding protein alpha chain
O15230	-1.3744676	0.2231664	8.637704	-6.158935	0.0001980	0.0055002	Laminin subunit alpha-5
Q9Y6X5	-1.4593292	0.2374461	8.653249	-6.145938	0.0001995	0.0055002	Bis(5-adenosyl)-triphosphatase ENPP4
Q7L4S7	-2.1135247	0.3024998	7.101207	-6.986862	0.0002003	0.0055002	Protein ARMCX6
P14550	-1.3048277	0.2159257	8.804116	-6.042949	0.0002101	0.0056911	Alcohol dehydrogenase [NADP(+)]
P23434	1.2727864	0.2182018	9.368515	5.833070	0.0002132	0.0057000	Glycine cleavage system H protein, mitochondrial
Q07954	-1.2959588	0.2228598	9.368515	-5.815132	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	0.2786106	9.173764	-5.866662	0.0002216	0.0057701	C-type mannose receptor 2
P49207	-1.3710319	0.2313344	8.972582	-5.926624	0.0002243	0.0057701	60S ribosomal protein L34
Q9BUF5	-1.7682813	0.3037349	9.249220	-5.821792	0.0002273	0.0057731	Tubulin beta-6 chain
P23142	-2.2973847	0.3519982	7.537201	-6.526695	0.0002373	0.0059527	Fibulin-1
P04196	-1.6877176	0.2571870	7.454498	-6.562221	0.0002403	0.0059550	Histidine-rich glycoprotein
Q9NRG4	2.3970480	0.3956883	8.368515	6.057919	0.0002533	0.0062001	N-lysine methyltransferase SMYD2
Q9NZ01	-1.8635396	0.3140808	8.634144	-5.933312	0.0002589	0.0062198	Very-long-chain enoyl-CoA reductase
O95980	-1.9294212	0.3147773	8.147873	-6.129480	0.0002602	0.0062198	Reversion-inducing cysteine-rich protein with Kazal motifs
P04275	-1.1968998	0.2066774	8.944173	-5.791150	0.0002687	0.0063480	von Willebrand factor;von Willebrand antigen 2
P12110	-1.5935296	0.2627341	8.170387	-6.065179	0.0002765	0.0064584	Collagen alpha-2(VI) chain
O75828	-1.4912698	0.2652157	9.368515	-5.622856	0.0002804	0.0064740	Carbonyl reductase [NADPH] 3
Q9BZH6	2.6654497	0.4489408	8.321746	5.937197	0.0002976	0.0066937	WD repeat-containing protein 11
P07357	-1.1909118	0.2117379	9.211049	-5.624461	0.0002977	0.0066937	Complement component C8 alpha chain
Q5JPH6	3.4079519	0.4420943	5.777444	7.708653	0.0002998	0.0066937	Probable glutamate–tRNA ligase, mitochondrial
Q86WV6	-1.1787564	0.2108725	9.223994	-5.589902	0.0003098	0.0068429	Stimulator of interferon genes protein
P24298	1.6449487	0.2841506	8.589351	5.789003	0.0003141	0.0068629	Alanine aminotransferase 1
P62760	-1.8748180	0.3363604	9.107922	-5.573837	0.0003312	0.0071471	Visinin-like protein 1
P01024	-1.1291448	0.2030574	9.105940	-5.560716	0.0003371	0.0071471	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	0.3221274	9.038732	-5.580064	0.0003377	0.0071471	Glutathione S-transferase theta-1
Q9UHG2	-2.3658698	0.4208485	8.845467	-5.621666	0.0003463	0.0072274	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
Q92681	-1.8052155	0.3015962	7.880492	-5.985538	0.0003486	0.0072274	Regulatory solute carrier protein family 1 member 1
Q9UQ35	-1.2247564	0.2246384	9.349254	-5.452123	0.0003543	0.0072730	Serine/arginine repetitive matrix protein 2
Q9HCB6	-2.0954145	0.3704513	8.642251	-5.656383	0.0003609	0.0073045	Spondin-1
P12814	-1.9016090	0.3261547	8.158010	-5.830390	0.0003635	0.0073045	Alpha-actinin-1
P48163	-1.9351889	0.3181025	7.573178	-6.083538	0.0003667	0.0073045	NADP-dependent malic enzyme
Q9Y3B4	-1.2875533	0.2342383	9.016576	-5.496767	0.0003793	0.0073267	Splicing factor 3B subunit 6
P25940	-1.6429098	0.3007556	9.103774	-5.462608	0.0003834	0.0073267	Collagen alpha-3(V) chain
P50453	-1.2078225	0.2193196	8.946744	-5.507133	0.0003847	0.0073267	Serpin B9
Q53GG5-2	-2.4399434	0.4282645	8.357999	-5.697282	0.0003883	0.0073267	PDZ and LIM domain protein 3
Q5M9N0	-2.7584485	0.4839467	8.333797	-5.699901	0.0003912	0.0073267	Coiled-coil domain-containing protein 158
P07585	-2.1323372	0.3937016	9.207909	-5.416125	0.0003919	0.0073267	Decorin
P49458	-1.8786710	0.3024079	7.199990	-6.212374	0.0003930	0.0073267	Signal recognition particle 9 kDa protein
P19429	2.2365865	0.3890156	8.159346	5.749349	0.0003991	0.0073720	Troponin I, cardiac muscle
Q53T59	-1.8080103	0.3112156	7.985793	-5.809511	0.0004035	0.0073862	HCLS1-binding protein 3
Q9UNW9	3.3060326	0.6124270	9.090331	5.398247	0.0004194	0.0076096	RNA-binding protein Nova-2
O94919	-1.1297756	0.2100853	9.132259	-5.377699	0.0004243	0.0076291	Endonuclease domain-containing 1 protein
P02747	-1.8530999	0.2972610	6.991839	-6.233915	0.0004328	0.0077151	Complement C1q subcomponent subunit C
P01008	-1.5453986	0.2920851	9.324724	-5.290919	0.0004444	0.0078523	Antithrombin-III
Q00G26	1.4810539	0.2508572	7.551962	5.903972	0.0004488	0.0078610	Perilipin-5
O00264	-1.4077482	0.2635473	9.045535	-5.341539	0.0004597	0.0079831	Membrane-associated progesterone receptor component 1
O60760	-2.2693850	0.4110516	8.368515	-5.520925	0.0004782	0.0081948	Hematopoietic prostaglandin D synthase
Q6SZW1	-2.0732831	0.3497058	7.368515	-5.928650	0.0004799	0.0081948	Sterile alpha and TIR motif-containing protein 1
Q9ULC3	-1.4313739	0.2659219	8.668837	-5.382685	0.0005031	0.0085188	Ras-related protein Rab-23
Q9BS26	-1.1794250	0.2270653	9.302987	-5.194210	0.0005110	0.0085813	Endoplasmic reticulum resident protein 44
Q8WZA9	-1.0848657	0.2080006	9.179407	-5.215686	0.0005182	0.0086202	Immunity-related GTPase family Q protein
P14543	-1.3732462	0.2627046	9.101457	-5.227339	0.0005244	0.0086202	Nidogen-1
P08603	-1.1479994	0.2226181	9.368515	-5.156810	0.0005260	0.0086202	Complement factor H
Q9BTV4	-1.5944595	0.3065562	9.159972	-5.201199	0.0005321	0.0086493	Transmembrane protein 43
Q2TAA5	-1.1153927	0.2188010	9.182611	-5.097748	0.0006078	0.0097840	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
P11586	1.2736427	0.2338157	7.997030	5.447207	0.0006115	0.0097840	C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
Q9UKR5	-3.6937409	0.7006297	8.496148	-5.272030	0.0006192	0.0098295	Probable ergosterol biosynthetic protein 28
Q9UJC5	-1.2143605	0.2412305	9.328442	-5.034026	0.0006323	0.0098619	SH3 domain-binding glutamic acid-rich-like protein 2
Q8WY22	-1.5074312	0.2849232	8.368515	-5.290657	0.0006356	0.0098619	BRI3-binding protein
P13671	-1.3576211	0.2703999	9.368515	-5.020790	0.0006358	0.0098619	Complement component C6
O14967	-1.6233066	0.3123389	8.528665	-5.197260	0.0006728	0.0103083	Calmegin
Q6PI78	1.5422623	0.3049907	9.040329	5.056752	0.0006747	0.0103083	Transmembrane protein 65
P01042	-1.9829048	0.3518050	7.254535	-5.636375	0.0006929	0.0105067	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q8WWQ0	-1.3446280	0.2726200	9.368515	-4.932242	0.0007203	0.0108219	PH-interacting protein
Q92621	-1.2226648	0.2480571	9.365549	-4.928965	0.0007243	0.0108219	Nuclear pore complex protein Nup205
Q12996	-1.6262833	0.2703540	6.441996	-6.015385	0.0007312	0.0108458	Cleavage stimulation factor subunit 3
Q9HAT2	1.5992357	0.3232883	9.219384	4.946779	0.0007400	0.0108568	Sialate O-acetylesterase
P20774	-1.9551933	0.3704552	8.018214	-5.277813	0.0007427	0.0108568	Mimecan
Q9BUH6	-1.0828646	0.2191138	9.144447	-4.942018	0.0007632	0.0110502	Protein PAXX
Q16082	-1.2629563	0.2540569	9.007531	-4.971155	0.0007668	0.0110502	Heat shock protein beta-2
Q8TDB4	-2.3381087	0.3845848	6.234194	-6.079566	0.0007800	0.0111612	Protein MGARP
P45877	-0.9878277	0.2031075	9.368515	-4.863571	0.0007941	0.0112837	Peptidyl-prolyl cis-trans isomerase C
Q14314	-1.9054905	0.3928504	9.365549	-4.850423	0.0008098	0.0113616	Fibroleukin
P35052	-1.2972987	0.2458088	7.795481	-5.277673	0.0008140	0.0113616	Glypican-1;Secreted glypican-1
P02461	-2.9334098	0.5758661	8.364929	-5.093909	0.0008163	0.0113616	Collagen alpha-1(III) chain
P02790	-1.3146905	0.2720008	9.354872	-4.833407	0.0008325	0.0115074	Hemopexin
P01034	-1.4676678	0.2965139	8.807288	-4.949744	0.0008440	0.0115885	Cystatin-C
Q86VP6	-1.3506010	0.2705182	8.501112	-4.992644	0.0008859	0.0119811	Cullin-associated NEDD8-dissociated protein 1
P40261	-1.4439118	0.2999907	9.222067	-4.813188	0.0008923	0.0119811	Nicotinamide N-methyltransferase
Q86VU5	1.3843626	0.2896972	9.368515	4.778653	0.0008967	0.0119811	Catechol O-methyltransferase domain-containing protein 1
P50479	-2.0822296	0.4095061	8.140181	-5.084733	0.0008983	0.0119811	PDZ and LIM domain protein 4
P28300	-1.4644405	0.2816798	7.773354	-5.198955	0.0009021	0.0119811	Protein-lysine 6-oxidase
P06727	-1.0726685	0.2190791	8.789110	-4.896261	0.0009129	0.0120458	Apolipoprotein A-IV
Q15126	-0.9960340	0.2092580	9.368515	-4.759837	0.0009213	0.0120786	Phosphomevalonate kinase
O95183	-1.4512639	0.3056654	9.368515	-4.747885	0.0009374	0.0121420	Vesicle-associated membrane protein 5
Q9HAV4	-1.8358132	0.3517014	7.618651	-5.219806	0.0009381	0.0121420	Exportin-5
Q9NRX4	1.4050508	0.2946685	9.219664	4.768243	0.0009518	0.0122406	14 kDa phosphohistidine phosphatase
Q96H79	-2.2370397	0.3813053	6.149079	-5.866794	0.0009938	0.0127004	Zinc finger CCCH-type antiviral protein 1-like
O43175	-2.0597036	0.4346867	9.169639	-4.738364	0.0010082	0.0127711	D-3-phosphoglycerate dehydrogenase
O43143	-0.8789725	0.1872152	9.368515	-4.694984	0.0010119	0.0127711	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
P13667	-1.0953363	0.2315013	9.120373	-4.731448	0.0010333	0.0129611	Protein disulfide-isomerase A4
P34932	-0.8861862	0.1892630	9.239908	-4.682301	0.0010698	0.0133366	Heat shock 70 kDa protein 4
Q15582	-2.2645249	0.4552254	8.016239	-4.974513	0.0010804	0.0133866	Transforming growth factor-beta-induced protein ig-h3
Q09161	1.9700086	0.3420465	6.161878	5.759476	0.0010883	0.0134025	Nuclear cap-binding protein subunit 1
Q9NY15	-1.4385610	0.3131081	9.351844	-4.594455	0.0011770	0.0143377	Stabilin-1
Q9UKX3	1.7720370	0.3830702	9.186578	4.625881	0.0011783	0.0143377	Myosin-13
P46940	-1.1105871	0.2405585	9.187975	-4.616702	0.0011935	0.0144363	Ras GTPase-activating-like protein IQGAP1
P00747	-0.8238672	0.1805037	9.354274	-4.564268	0.0012294	0.0147814	Plasminogen;Plasmin heavy chain A;Activation peptide;Angiostatin;Plasmin heavy chain A, short form;Plasmin light chain B
P26447	-1.4990741	0.3198741	8.706709	-4.686450	0.0012486	0.0149246	Protein S100-A4
O60262	-1.2559109	0.2675648	8.648172	-4.693856	0.0012587	0.0149574	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
Q96CS3	-1.1510089	0.2499576	9.039642	-4.604817	0.0012670	0.0149688	FAS-associated factor 2
Q6UWS5	1.3529266	0.2662058	7.240188	5.082259	0.0012889	0.0151389	Protein PET117 homolog, mitochondrial
P01019	-1.0239723	0.2238020	9.075475	-4.575349	0.0013081	0.0152758	Angiotensinogen;Angiotensin-1;Angiotensin-2;Angiotensin-3;Angiotensin-4;Angiotensin 1-9;Angiotensin 1-7;Angiotensin 1-5;Angiotensin 1-4
O95445	-2.5298428	0.5528034	9.049917	-4.576388	0.0013157	0.0152771	Apolipoprotein M
P27658	-1.6133702	0.3584618	9.368515	-4.500815	0.0013446	0.0154858	Collagen alpha-1(VIII) chain;Vastatin
Q96JB2	-2.0512914	0.4356460	8.368515	-4.708620	0.0013489	0.0154858	Conserved oligomeric Golgi complex subunit 3
Q07507	-1.2545210	0.2597851	7.876778	-4.829072	0.0013648	0.0155371	Dermatopontin
Q9BXV9	1.4430515	0.3197648	9.237464	4.512853	0.0013687	0.0155371	Uncharacterized protein C14orf142
P09619	-1.2391198	0.2747061	9.174768	-4.510711	0.0013968	0.0157678	Platelet-derived growth factor receptor beta
P02748	-1.2229145	0.2680588	8.861132	-4.562113	0.0014178	0.0159171	Complement component C9;Complement component C9a;Complement component C9b
Q96LL9	-1.2440322	0.2732652	8.758485	-4.552471	0.0014809	0.0165339	DnaJ homolog subfamily C member 30
Q04721	1.1483233	0.2577713	9.161674	4.454814	0.0015208	0.0168869	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
Q92930	-1.4774889	0.3068323	7.610113	-4.815297	0.0015297	0.0168928	Ras-related protein Rab-8B
Q9UQR1	-1.7724910	0.3594745	7.181954	-4.930784	0.0015718	0.0172051	Zinc finger protein 148
P54577	-1.0184999	0.2282130	8.964834	-4.462936	0.0015859	0.0172051	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
O95486	-1.3819063	0.3110275	9.026357	-4.443036	0.0016048	0.0172051	Protein transport protein Sec24A
Q99983	-2.9528995	0.5887154	6.898086	-5.015835	0.0016058	0.0172051	Osteomodulin
P83916	-1.6056296	0.3062406	6.368515	-5.243034	0.0016076	0.0172051	Chromobox protein homolog 1
P03950	-1.7791248	0.3843836	8.153301	-4.628514	0.0016087	0.0172051	Angiogenin
Q9UBV8	-1.1380629	0.2554637	8.905453	-4.454890	0.0016309	0.0173507	Peflin
P15924	0.9266546	0.2127436	9.331901	4.355733	0.0016841	0.0177485	Desmoplakin
Q7Z3T8	-1.3746348	0.3051521	8.534300	-4.504753	0.0016906	0.0177485	Zinc finger FYVE domain-containing protein 16
P00352	-1.1346512	0.2480808	8.199505	-4.573716	0.0017048	0.0177485	Retinal dehydrogenase 1
Q9H1E5	-1.0067111	0.2320392	9.368515	-4.338539	0.0017122	0.0177485	Thioredoxin-related transmembrane protein 4
O75489	1.0163873	0.2345130	9.368515	4.334033	0.0017238	0.0177485	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
O15061	-1.1041834	0.2548567	9.368515	-4.332565	0.0017276	0.0177485	Synemin
P62857	-1.3551185	0.2882394	7.661559	-4.701365	0.0017294	0.0177485	40S ribosomal protein S28
P80723	-1.5107829	0.3279300	7.975567	-4.607029	0.0017534	0.0178587	Brain acid soluble protein 1
Q9NS69	-1.0847694	0.2446484	8.743555	-4.433993	0.0017577	0.0178587	Mitochondrial import receptor subunit TOM22 homolog
P19447	-1.5879548	0.3333670	7.368515	-4.763383	0.0017822	0.0180166	TFIIH basal transcription factor complex helicase XPB subunit
Q96CX2	-0.9045513	0.2094108	9.289387	-4.319506	0.0017970	0.0180770	BTB/POZ domain-containing protein KCTD12
Q9NS86	-0.9960486	0.2292502	9.072623	-4.344811	0.0018293	0.0183114	LanC-like protein 2
P52907	-0.8523732	0.1990185	9.368515	-4.282883	0.0018618	0.0185310	F-actin-capping protein subunit alpha-1
Q08945	-1.3761500	0.3080482	8.368515	-4.467320	0.0018695	0.0185310	FACT complex subunit SSRP1
Q9BYN0	-1.2801043	0.2972043	9.119551	-4.307153	0.0019105	0.0187226	Sulfiredoxin-1
O15118	-2.1247916	0.4187335	6.368515	-5.074329	0.0019107	0.0187226	Niemann-Pick C1 protein
Q9UBB5	1.4388020	0.2837099	6.368515	5.071384	0.0019165	0.0187226	Methyl-CpG-binding domain protein 2
P62328	-1.3455146	0.2882781	7.467526	-4.667418	0.0019323	0.0187251	Thymosin beta-4;Hematopoietic system regulatory peptide
Q9Y287	-1.6105936	0.3774229	9.306232	-4.267344	0.0019352	0.0187251	Integral membrane protein 2B;BRI2, membrane form;BRI2 intracellular domain;BRI2C, soluble form;Bri23 peptide
Q8N142	1.0768090	0.2519306	9.227805	4.274229	0.0019526	0.0188043	Adenylosuccinate synthetase isozyme 1
Q14118	-0.8487363	0.1948314	8.729896	-4.356260	0.0019708	0.0188897	Dystroglycan;Alpha-dystroglycan;Beta-dystroglycan
P82663	-1.3399129	0.3163371	9.321073	-4.235712	0.0020224	0.0192935	28S ribosomal protein S25, mitochondrial
P31323	-0.9232942	0.2175357	9.197017	-4.244333	0.0020574	0.0194504	cAMP-dependent protein kinase type II-beta regulatory subunit
Q8NAT1	-0.8308927	0.1966105	9.308991	-4.226085	0.0020580	0.0194504	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Q07065	-0.9488623	0.2217110	8.907887	-4.279726	0.0020997	0.0196636	Cytoskeleton-associated protein 4
P61009	-0.8882212	0.2043041	8.543558	-4.347545	0.0020999	0.0196636	Signal peptidase complex subunit 3
P50991	-1.5101244	0.3455691	8.412399	-4.369963	0.0021113	0.0196794	T-complex protein 1 subunit delta
P07384	-0.8641607	0.2057730	9.249572	-4.199582	0.0021727	0.0201592	Calpain-1 catalytic subunit
Q6IC98	-0.9057366	0.2103133	8.604001	-4.306605	0.0021886	0.0202149	GRAM domain-containing protein 4
A5D6W6	-2.1994339	0.4938411	7.797294	-4.453728	0.0022680	0.0207816	Fat storage-inducing transmembrane protein 1
P05455	-0.8562036	0.2042908	9.119319	-4.191102	0.0022704	0.0207816	Lupus La protein
Q96AG4	-1.0641384	0.2559899	9.298006	-4.156954	0.0022911	0.0208771	Leucine-rich repeat-containing protein 59
Q12988	-1.0103210	0.2428996	9.203748	-4.159418	0.0023336	0.0211689	Heat shock protein beta-3
Q04760	1.3958984	0.3310671	8.731244	4.216360	0.0024092	0.0217575	Lactoylglutathione lyase
P13796	-0.8819572	0.2124403	9.077821	-4.151553	0.0024329	0.0217925	Plastin-2
Q8IYI6	-0.9330152	0.2271103	9.357653	-4.108203	0.0024345	0.0217925	Exocyst complex component 8
P62277	-1.3005300	0.3165707	9.329038	-4.108181	0.0024504	0.0218387	40S ribosomal protein S13
P61925	1.3913131	0.3116808	7.494591	4.463904	0.0024686	0.0218532	cAMP-dependent protein kinase inhibitor alpha
P50238	-1.7621993	0.4213329	8.809214	-4.182439	0.0024817	0.0218532	Cysteine-rich protein 1
Q9H1K0	-1.6022771	0.3566592	7.368515	-4.492460	0.0024843	0.0218532	Rabenosyn-5
Q96A65	-0.8321129	0.2036279	9.365549	-4.086438	0.0025127	0.0220078	Exocyst complex component 4
P05543	-1.1801143	0.2627223	7.296856	-4.491870	0.0025476	0.0222175	Thyroxine-binding globulin
Q9UK22	-1.3974278	0.2914940	6.360323	-4.794019	0.0025763	0.0223721	F-box only protein 2
Q9Y490	-0.8597753	0.2099641	9.136720	-4.094869	0.0026129	0.0225934	Talin-1
P62745	-1.1929691	0.2867990	8.678045	-4.159600	0.0026513	0.0228280	Rho-related GTP-binding protein RhoB
P24311	1.1056319	0.2733972	9.368515	4.044050	0.0026803	0.0229807	Cytochrome c oxidase subunit 7B, mitochondrial
O00625	-1.1028338	0.2729250	9.368515	-4.040795	0.0026938	0.0229958	Pirin
P58546	-1.2963604	0.3154621	8.897011	-4.109402	0.0027047	0.0229958	Myotrophin
O75348	-1.2891767	0.3199876	9.368515	-4.028833	0.0027440	0.0231999	V-type proton ATPase subunit G 1
Q96FN9	-1.7766077	0.4240713	8.368515	-4.189407	0.0027516	0.0231999	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
P04843	-1.5241453	0.3687786	8.620081	-4.132955	0.0027960	0.0234770	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
P63316	0.8794535	0.2197962	9.368515	4.001223	0.0028637	0.0236219	Troponin C, slow skeletal and cardiac muscles
Q9UL18	-1.3184619	0.3094006	7.861683	-4.261343	0.0028685	0.0236219	Protein argonaute-1
Q9HB40	-1.4736038	0.3126963	6.309415	-4.712572	0.0028735	0.0236219	Retinoid-inducible serine carboxypeptidase
Q9Y4W6	0.9189304	0.2288559	9.244730	4.015324	0.0028784	0.0236219	AFG3-like protein 2
Q96C86	-0.8529077	0.2113460	9.097353	-4.035599	0.0028837	0.0236219	m7GpppX diphosphatase
Q8N5M1	-1.2833584	0.3177267	9.071102	-4.039190	0.0028851	0.0236219	ATP synthase mitochondrial F1 complex assembly factor 2
Q96GK7	-1.2557512	0.2951067	7.858601	-4.255244	0.0028946	0.0236219	Fumarylacetoacetate hydrolase domain-containing protein 2A
Q6P1N0	-1.6508051	0.3683246	6.930592	-4.481930	0.0029313	0.0237644	Coiled-coil and C2 domain-containing protein 1A
Q3ZCW2	-1.3933792	0.3090667	6.831572	-4.508345	0.0029448	0.0237644	Galectin-related protein
Q9NQZ5	1.3550021	0.3369968	9.100196	4.020816	0.0029472	0.0237644	StAR-related lipid transfer protein 7, mitochondrial
Q9UKS6	0.9882506	0.2447159	8.940065	4.038359	0.0029764	0.0238244	Protein kinase C and casein kinase substrate in neurons protein 3
P00492	-0.9642312	0.2388890	8.951031	-4.036314	0.0029780	0.0238244	Hypoxanthine-guanine phosphoribosyltransferase
Q15125	-1.5522594	0.3852969	8.979444	-4.028736	0.0029926	0.0238469	3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Q9NNX1	3.4412993	0.7418771	6.368515	4.638638	0.0030383	0.0240453	Tuftelin
Q00577	-1.0249972	0.2547767	8.945807	-4.023119	0.0030412	0.0240453	Transcriptional activator protein Pur-alpha
Q53FA7	1.3758827	0.3472331	9.148525	3.962419	0.0031873	0.0251030	Quinone oxidoreductase PIG3
P14555	-3.1616763	0.7154939	6.864718	-4.418872	0.0032350	0.0253806	Phospholipase A2, membrane associated
Q9UHD9	-0.8978150	0.2264057	9.029337	-3.965514	0.0032557	0.0254020	Ubiquilin-2
P25311	-1.0782056	0.2665443	8.504397	-4.045128	0.0032670	0.0254020	Zinc-alpha-2-glycoprotein
O95810	-0.7267426	0.1854626	9.339643	-3.918540	0.0032756	0.0254020	Serum deprivation-response protein
P09467	-1.4304382	0.3321100	7.221982	-4.307122	0.0032878	0.0254020	Fructose-1,6-bisphosphatase 1
P50552	-0.9233883	0.2330031	8.984989	-3.962987	0.0033003	0.0254020	Vasodilator-stimulated phosphoprotein
P01303	-1.3886725	0.3517627	8.938580	-3.947754	0.0034118	0.0260658	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
P53618	-0.9076351	0.2334115	9.368515	-3.888561	0.0034122	0.0260658	Coatomer subunit beta
Q7L4E1	-1.9056994	0.4891450	9.152083	-3.895980	0.0035267	0.0266923	Protein FAM73B
O15031	-0.9094327	0.2323003	9.006842	-3.914900	0.0035331	0.0266923	Plexin-B2
Q9BVC6	-1.1958920	0.3093192	9.368515	-3.866207	0.0035336	0.0266923	Transmembrane protein 109
Q92575	-0.9922287	0.2514210	8.704054	-3.946483	0.0036021	0.0269450	UBX domain-containing protein 4
P28070	-0.9263111	0.2265329	7.880089	-4.089080	0.0036037	0.0269450	Proteasome subunit beta type-4
Q8IYU8	-3.0629900	0.6834395	6.368515	-4.481728	0.0036143	0.0269450	Calcium uptake protein 2, mitochondrial
Q96MM6	1.8061841	0.4127928	6.692352	4.375523	0.0036201	0.0269450	Heat shock 70 kDa protein 12B
Q7KZF4	-0.8794696	0.2290501	9.368515	-3.839639	0.0036838	0.0272453	Staphylococcal nuclease domain-containing protein 1
P21980	-0.9178411	0.2354438	8.925059	-3.898346	0.0036872	0.0272453	Protein-glutamine gamma-glutamyltransferase 2
Q14258	-0.9919848	0.2475034	8.199522	-4.007964	0.0037143	0.0273462	E3 ubiquitin/ISG15 ligase TRIM25
A6NDG6	1.0711621	0.2778811	9.119206	3.854750	0.0037836	0.0275442	Phosphoglycolate phosphatase
Q8IUX7	-2.3978246	0.4997419	5.506029	-4.798126	0.0037891	0.0275442	Adipocyte enhancer-binding protein 1
P43121	-1.0780079	0.2729286	8.460052	-3.949780	0.0037919	0.0275442	Cell surface glycoprotein MUC18
P14625	-0.9671286	0.2529912	9.351322	-3.822776	0.0037955	0.0275442	Endoplasmin
P10109	0.8708452	0.2262157	9.123936	3.849623	0.0038099	0.0275506	Adrenodoxin, mitochondrial
Q9Y2D4	-1.5165389	0.3883438	8.670699	-3.905145	0.0038589	0.0277544	Exocyst complex component 6B
P27695	-1.4919668	0.3916934	9.368515	-3.809017	0.0038654	0.0277544	DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial
E5RK69	-1.1254137	0.2963660	9.368515	-3.797378	0.0039369	0.0281680	Annexin
Q96PK6	-0.9252023	0.2414612	9.066841	-3.831680	0.0039627	0.0282430	RNA-binding protein 14
Q9Y5U8	-2.4800568	0.6520088	9.267735	-3.803717	0.0039751	0.0282430	Mitochondrial pyruvate carrier 1
Q15738	-1.0818010	0.2856470	9.368515	-3.787196	0.0040005	0.0283243	Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
Q9BWJ5	-1.1786521	0.3118418	9.368515	-3.779648	0.0040484	0.0285637	Splicing factor 3B subunit 5
Q01581	-1.5736067	0.3810212	7.264691	-4.129971	0.0040639	0.0285737	Hydroxymethylglutaryl-CoA synthase, cytoplasmic
P62312	-1.5682756	0.4058646	8.682788	-3.864037	0.0040916	0.0286287	U6 snRNA-associated Sm-like protein LSm6
P31949	-0.9710473	0.2572068	9.320482	-3.775357	0.0041136	0.0286287	Protein S100-A11;Protein S100-A11, N-terminally processed
P04207	-1.4064185	0.3678959	8.921399	-3.822871	0.0041385	0.0286287	Ig kappa chain V-III region CLL
P78406	-1.6990379	0.3860209	6.248772	-4.401414	0.0041396	0.0286287	mRNA export factor
P49773	-0.9406572	0.2498333	9.368515	-3.765139	0.0041421	0.0286287	Histidine triad nucleotide-binding protein 1
P27169	-1.0408608	0.2721419	8.886557	-3.824700	0.0041569	0.0286334	Serum paraoxonase/arylesterase 1
Q13636	-1.9750968	0.4475747	6.181801	-4.412887	0.0041942	0.0287929	Ras-related protein Rab-31
Q96EM0	-1.2281296	0.3139401	8.248715	-3.911987	0.0042092	0.0287984	Trans-3-hydroxy-L-proline dehydratase
Q2TAY7	-1.0380001	0.2740649	9.064251	-3.787425	0.0042446	0.0289045	WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed
Q9BT09	-1.2017444	0.3172898	9.053373	-3.787530	0.0042532	0.0289045	Protein canopy homolog 3
P01699	-1.9617461	0.4491212	6.250045	-4.367966	0.0042950	0.0290912	Ig lambda chain V-I region VOR
P00488	-1.1450813	0.3057007	9.222895	-3.745760	0.0043905	0.0296393	Coagulation factor XIII A chain
Q04941	-1.3354806	0.3552191	9.070341	-3.759597	0.0044259	0.0297432	Proteolipid protein 2
P01611	-1.3210912	0.3549489	9.368515	-3.721919	0.0044351	0.0297432	Ig kappa chain V-I region Wes
P07360	-0.9508577	0.2503895	8.706976	-3.797514	0.0044972	0.0299271	Complement component C8 gamma chain
O75165	-0.7578962	0.2029693	9.179846	-3.734044	0.0045087	0.0299271	DnaJ homolog subfamily C member 13
Q9BXF6	-0.8964783	0.2416746	9.368515	-3.709444	0.0045237	0.0299271	Rab11 family-interacting protein 5
Q02818	-1.1067621	0.2686961	6.943204	-4.119011	0.0045442	0.0299271	Nucleobindin-1
Q9UNN8	-1.2379487	0.3234874	8.454603	-3.826884	0.0045452	0.0299271	Endothelial protein C receptor
Q96KP1	-1.0392328	0.2563923	7.216104	-4.053292	0.0045509	0.0299271	Exocyst complex component 2
P46063	-0.7705141	0.2065451	9.131319	-3.730488	0.0045761	0.0299956	ATP-dependent DNA helicase Q1
Q9HBL0	1.0363941	0.2703946	8.368515	3.832895	0.0045923	0.0299978	Tensin-1
P20042	-0.8792944	0.2360783	9.145397	-3.724588	0.0046060	0.0299978	Eukaryotic translation initiation factor 2 subunit 2
Q8IVD9	-0.9380220	0.2431350	8.146885	-3.858029	0.0046582	0.0301927	NudC domain-containing protein 3
Q13011	0.8580498	0.2280683	8.786732	3.762249	0.0046656	0.0301927	Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Q5JUQ0	2.8054144	0.6820706	6.812210	4.113085	0.0047695	0.0307667	Protein FAM78A
P10643	-1.1503065	0.3105471	9.107891	-3.704129	0.0047894	0.0307978	Complement component C7
Q9Y5U9	-0.9688010	0.2518740	8.062092	-3.846372	0.0048314	0.0308069	Immediate early response 3-interacting protein 1
P31689	-1.4848105	0.3869055	8.103416	-3.837657	0.0048449	0.0308069	DnaJ homolog subfamily A member 1
Q53GG5	1.0396066	0.2790390	8.863381	3.725668	0.0048577	0.0308069	PDZ and LIM domain protein 3
Q04837	-1.2706968	0.3379158	8.599329	-3.760395	0.0048634	0.0308069	Single-stranded DNA-binding protein, mitochondrial
Q9BU61	-1.2937160	0.3532972	9.368515	-3.661835	0.0048791	0.0308069	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3
Q9BXR6	-1.3408193	0.3662422	9.365549	-3.661018	0.0048880	0.0308069	Complement factor H-related protein 5
Q08357	-1.2512681	0.3308816	8.413610	-3.781619	0.0049024	0.0308069	Sodium-dependent phosphate transporter 2
Q9HCN8	-0.8376149	0.2283304	9.273239	-3.668434	0.0049121	0.0308069	Stromal cell-derived factor 2-like protein 1
Q8NDY3	1.2548368	0.3406660	9.014277	3.683481	0.0050345	0.0314287	[Protein ADP-ribosylarginine] hydrolase-like protein 1
P61020	-0.8349426	0.2253006	8.815114	-3.705906	0.0050548	0.0314287	Ras-related protein Rab-5B
P00918	-0.9493414	0.2601140	9.275546	-3.649713	0.0050577	0.0314287	Carbonic anhydrase 2
Q8TDB6	-0.9819803	0.2672730	9.050201	-3.674073	0.0050741	0.0314345	E3 ubiquitin-protein ligase DTX3L
P31994-2	-0.7713913	0.2103426	9.070422	-3.667309	0.0051084	0.0315512	Low affinity immunoglobulin gamma Fc region receptor II-b
Q8NBF2	-0.8115466	0.2231788	9.295600	-3.636307	0.0051478	0.0315923	NHL repeat-containing protein 2
O00299	-0.9153236	0.2514532	9.252980	-3.640136	0.0051558	0.0315923	Chloride intracellular channel protein 1
Q9UBI9	-1.9350473	0.4881616	7.179374	-3.963948	0.0051638	0.0315923	Headcase protein homolog
O75663	-1.6975991	0.4619527	8.937706	-3.674833	0.0051773	0.0315923	TIP41-like protein
Q9Y5J7	-1.4394711	0.3975400	9.368515	-3.620946	0.0052076	0.0316822	Mitochondrial import inner membrane translocase subunit Tim9
Q8WUM0	-0.7928646	0.2184077	9.225248	-3.630204	0.0052636	0.0318998	Nuclear pore complex protein Nup133
O15121	-1.3734454	0.3779039	9.176918	-3.634377	0.0052748	0.0318998	Sphingolipid delta(4)-desaturase DES1
P00742	-1.3361965	0.3240987	6.367292	-4.122808	0.0054523	0.0328758	Coagulation factor X;Factor X light chain;Factor X heavy chain;Activated factor Xa heavy chain
P46777	-1.0578875	0.2886020	8.705364	-3.665559	0.0054928	0.0330217	60S ribosomal protein L5
Q6P1L8	0.6856534	0.1900803	9.150911	3.607177	0.0055315	0.0331366	39S ribosomal protein L14, mitochondrial
P49756	-0.8733625	0.2438382	9.368515	-3.581729	0.0055445	0.0331366	RNA-binding protein 25
Q15493	-1.5865116	0.4375794	8.953910	-3.625654	0.0055701	0.0331921	Regucalcin
O00567	-1.6066654	0.4490317	9.293824	-3.578067	0.0056491	0.0335642	Nucleolar protein 56
Q9H4A6	-0.9863755	0.2760422	9.281309	-3.573278	0.0057047	0.0337956	Golgi phosphoprotein 3
Q6PCE3	-1.3068366	0.3388515	7.308933	-3.856665	0.0057421	0.0338380	Glucose 1,6-bisphosphate synthase
P24752	0.8145171	0.2252393	8.863954	3.616231	0.0057474	0.0338380	Acetyl-CoA acetyltransferase, mitochondrial
O15144	-1.0266458	0.2834111	8.799457	-3.622462	0.0057618	0.0338380	Actin-related protein 2/3 complex subunit 2
Q9Y646	-0.6906706	0.1939266	9.242400	-3.561506	0.0058516	0.0342667	Carboxypeptidase Q
Q1KMD3	-0.9588418	0.2678819	9.013577	-3.579346	0.0059224	0.0345813	Heterogeneous nuclear ribonucleoprotein U-like protein 2
P06396	-1.1557324	0.3165530	8.403242	-3.650991	0.0059628	0.0347174	Gelsolin
P56199	-0.8817502	0.2433801	8.591843	-3.622935	0.0059912	0.0347281	Integrin alpha-1
P62330	-0.7931556	0.2225041	9.070930	-3.564678	0.0059988	0.0347281	ADP-ribosylation factor 6
Q9HAN9	1.2305740	0.3215603	7.269312	3.826884	0.0060368	0.0347644	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Q96PE7	-1.1472298	0.3251386	9.368515	-3.528434	0.0060393	0.0347644	Methylmalonyl-CoA epimerase, mitochondrial
P17050	-0.9454418	0.2670070	9.104364	-3.540888	0.0061917	0.0355410	Alpha-N-acetylgalactosaminidase
Q9UBS4	-1.7470606	0.4933708	8.992939	-3.541070	0.0063113	0.0361182	DnaJ homolog subfamily B member 11
Q9H9B4	-0.7776690	0.2176678	8.706871	-3.572734	0.0063278	0.0361182	Sideroflexin-1
Q8TCJ2	-0.8698436	0.2449287	8.869231	-3.551416	0.0063483	0.0361335	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit STT3B
P62191	-1.0000517	0.2845330	9.150000	-3.514713	0.0064034	0.0363282	26S protease regulatory subunit 4
Q9Y5Z7	-1.9019574	0.4671411	6.064616	-4.071484	0.0064182	0.0363282	Host cell factor 2
P01597	-2.2333895	0.6336670	8.991128	-3.524548	0.0064791	0.0365707	Ig kappa chain V-I region DEE
P23284	-0.7744408	0.2195725	8.930613	-3.527040	0.0065225	0.0367138	Peptidyl-prolyl cis-trans isomerase B
P05062	-2.0647894	0.5509893	7.365549	-3.747422	0.0065557	0.0367988	Fructose-bisphosphate aldolase B
P60903	-0.8289441	0.2370745	9.149846	-3.496555	0.0065908	0.0368796	Protein S100-A10
O43920	0.8295850	0.2371029	9.112623	3.498840	0.0066082	0.0368796	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
Q68DH5	-0.9839434	0.2736831	8.292742	-3.595192	0.0066245	0.0368796	LMBR1 domain-containing protein 2
P08754	-1.0292580	0.2970305	9.368515	-3.465159	0.0066871	0.0369628	Guanine nucleotide-binding protein G(k) subunit alpha
O75643	-0.7286175	0.2103421	9.368515	-3.463964	0.0067000	0.0369628	U5 small nuclear ribonucleoprotein 200 kDa helicase
Q9HAV7	0.8532336	0.2444747	9.112699	3.490070	0.0067006	0.0369628	GrpE protein homolog 1, mitochondrial
P15848	0.9204565	0.2587601	8.518770	3.557181	0.0067122	0.0369628	Arylsulfatase B
P30050	-1.1309945	0.3250772	9.188767	-3.479157	0.0067322	0.0369723	60S ribosomal protein L12
P17540	0.9216483	0.2461009	7.246829	3.745002	0.0067743	0.0370720	Creatine kinase S-type, mitochondrial
P27797	-0.8755252	0.2533742	9.365549	-3.455464	0.0067958	0.0370720	Calreticulin
O14807	-0.9860449	0.2835215	9.126236	-3.477849	0.0068164	0.0370720	Ras-related protein M-Ras
O43290	-0.7436611	0.2154130	9.368515	-3.452257	0.0068279	0.0370720	U4/U6.U5 tri-snRNP-associated protein 1
P98160	-0.6944147	0.2002054	9.194052	-3.468511	0.0068415	0.0370720	Basement membrane-specific heparan sulfate proteoglycan core protein;Endorepellin;LG3 peptide
Q9GZY4	-1.6172207	0.4429683	7.724104	-3.650873	0.0068891	0.0371704	Cytochrome c oxidase assembly factor 1 homolog
Q16204	-0.7607082	0.2170359	8.804087	-3.504989	0.0069024	0.0371704	Coiled-coil domain-containing protein 6
Q14019	-2.3417241	0.5970441	6.368515	-3.922196	0.0069146	0.0371704	Coactosin-like protein
O75190-3	1.2231318	0.3561256	9.368515	3.434552	0.0070261	0.0375719	DnaJ homolog subfamily B member 6
Q9Y623	-1.9955095	0.5624635	8.347526	-3.547803	0.0070339	0.0375719	Myosin-4
P30101	-0.7361350	0.2143226	9.350033	-3.434705	0.0070447	0.0375719	Protein disulfide-isomerase A3
Q12907	-1.6602075	0.4672046	8.262135	-3.553491	0.0070910	0.0377197	Vesicular integral-membrane protein VIP36
O75533	-0.7480960	0.2181250	9.229376	-3.429667	0.0072389	0.0383395	Splicing factor 3B subunit 1
P21281	-1.3428216	0.3926752	9.325789	-3.419675	0.0072453	0.0383395	V-type proton ATPase subunit B, brain isoform
Q6ZVF9	-1.5316163	0.3683301	5.459015	-4.158271	0.0073138	0.0386019	G protein-regulated inducer of neurite outgrowth 3
P41208	-1.1048997	0.3218685	9.069961	-3.432767	0.0073904	0.0389048	Centrin-2
P32119	-0.8759792	0.2446886	7.845250	-3.579976	0.0074241	0.0389814	Peroxiredoxin-2
P55735	-0.9148870	0.2645670	8.693582	-3.458054	0.0075682	0.0395989	Protein SEC13 homolog
P56192	-1.0251690	0.2974827	8.778730	-3.446146	0.0075968	0.0395989	Methionine–tRNA ligase, cytoplasmic
Q5VUM1	0.7587056	0.2227605	9.162066	3.405926	0.0076002	0.0395989	Succinate dehydrogenase assembly factor 4, mitochondrial
Q8NBJ5	-1.0090957	0.2920525	8.662097	-3.455185	0.0076436	0.0396399	Procollagen galactosyltransferase 1
O43707	-1.3709413	0.3948544	8.502779	-3.472018	0.0076624	0.0396399	Alpha-actinin-4
P11021	-0.6930674	0.2026785	8.964949	-3.419540	0.0076773	0.0396399	78 kDa glucose-regulated protein
P02749	-0.9821379	0.2870969	8.944681	-3.420929	0.0076861	0.0396399	Beta-2-glycoprotein 1
Q92805	1.3677629	0.3987991	8.806786	3.429704	0.0077571	0.0398243	Golgin subfamily A member 1
Q96G03	-0.8738839	0.2590704	9.368515	-3.373152	0.0077610	0.0398243	Phosphoglucomutase-2
Q9UK41	-1.5562781	0.4608152	9.216740	-3.377228	0.0078906	0.0403869	Vacuolar protein sorting-associated protein 28 homolog
P61026	-0.8659400	0.2419876	7.550336	-3.578447	0.0079279	0.0404763	Ras-related protein Rab-10
P43686	-1.2985795	0.3872675	9.346257	-3.353185	0.0080435	0.0409059	26S protease regulatory subunit 6B
Q6Y288	-1.0690665	0.3176467	9.206542	-3.365583	0.0080524	0.0409059	Beta-1,3-glucosyltransferase
Q9BVG4	-1.4282890	0.4270144	9.367831	-3.344827	0.0081274	0.0411504	Protein PBDC1
Q9UBQ0	-1.1043560	0.3287126	9.187820	-3.359640	0.0081530	0.0411504	Vacuolar protein sorting-associated protein 29
Q6ICB0	-2.0382992	0.5474803	6.643568	-3.723055	0.0081612	0.0411504	Desumoylating isopeptidase 1
O60568	-1.0635431	0.3196277	9.368515	-3.327443	0.0083597	0.0419548	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Q5T447	-1.0258262	0.3034558	8.818363	-3.380480	0.0083620	0.0419548	E3 ubiquitin-protein ligase HECTD3
P17174	0.8269867	0.2471121	9.140033	3.346605	0.0083865	0.0419739	Aspartate aminotransferase, cytoplasmic
Q14011	-1.6060873	0.4676159	8.235300	-3.434629	0.0085122	0.0424981	Cold-inducible RNA-binding protein
Q9BSH5	-0.8065712	0.2403739	8.926460	-3.355486	0.0085480	0.0425722	Haloacid dehalogenase-like hydrolase domain-containing protein 3
Q9HCJ6	-0.8677868	0.2621555	9.365549	-3.310199	0.0086016	0.0427344	Synaptic vesicle membrane protein VAT-1 homolog-like
P16455	-0.7988054	0.2337279	8.299782	-3.417673	0.0086305	0.0427738	Methylated-DNA–protein-cysteine methyltransferase
Q96LD4	-2.0603233	0.5321496	5.836190	-3.871700	0.0087047	0.0429367	Tripartite motif-containing protein 47
Q9BX97	-1.3847012	0.3968594	7.706232	-3.489148	0.0087057	0.0429367	Plasmalemma vesicle-associated protein
P29992	-1.0018710	0.2947420	8.384398	-3.399146	0.0087438	0.0430202	Guanine nucleotide-binding protein subunit alpha-11
P05387	-0.7447264	0.2248827	9.209711	-3.311622	0.0087797	0.0430925	60S acidic ribosomal protein P2
P51692	-1.6950637	0.5100261	9.048184	-3.323484	0.0088256	0.0432133	Signal transducer and activator of transcription 5B
O60927	-0.9472893	0.2647529	7.020703	-3.578013	0.0089556	0.0437412	Protein phosphatase 1 regulatory subunit 11
A4D2B0	-1.7140517	0.5058266	8.315238	-3.388615	0.0089934	0.0437412	Metallo-beta-lactamase domain-containing protein 1
P16083	-1.0028849	0.2964031	8.356423	-3.383517	0.0089980	0.0437412	Ribosyldihydronicotinamide dehydrogenase [quinone]
Q13425	-0.7615654	0.2315077	9.255655	-3.289589	0.0090372	0.0438273	Beta-2-syntrophin
I3L505	1.1922390	0.3573157	8.690314	3.336654	0.0091435	0.0442372	Acyl carrier protein
Q9NX08	-0.7274661	0.2206444	8.946597	-3.297007	0.0093494	0.0450351	COMM domain-containing protein 8
Q96CN7	-1.0144660	0.3094032	9.139815	-3.278783	0.0093528	0.0450351	Isochorismatase domain-containing protein 1
O43592	-0.8026366	0.2463151	9.275503	-3.258576	0.0094768	0.0454806	Exportin-T
Q8N392	2.3552996	0.6371457	6.220195	3.696642	0.0094949	0.0454806	Rho GTPase-activating protein 18
P01621	-1.1890923	0.3617739	8.939202	-3.286838	0.0095124	0.0454806	Ig kappa chain V-III region NG9
Q9UMR3	-1.6328959	0.4711365	7.368515	-3.465866	0.0096536	0.0460471	T-box transcription factor TBX20
P35754	0.8371729	0.2577884	9.204719	3.247520	0.0097457	0.0463777	Glutaredoxin-1
O60503	1.2572380	0.3410186	6.155432	3.686714	0.0097914	0.0464861	Adenylate cyclase type 9
Q13825	1.3948092	0.4331033	9.368515	3.220500	0.0099550	0.0471527	Methylglutaconyl-CoA hydratase, mitochondrial
O95159	-1.7663091	0.5270945	8.009301	-3.351029	0.0100480	0.0474828	Zinc finger protein-like 1
Q8IWU2	-0.7035098	0.2110972	8.107735	-3.332635	0.0101485	0.0477214	Serine/threonine-protein kinase LMTK2
Q6B0K9	-1.3448839	0.3993022	7.802404	-3.368085	0.0101788	0.0477214	Hemoglobin subunit mu
Q13541	0.9175109	0.2861883	9.368515	3.205969	0.0101948	0.0477214	Eukaryotic translation initiation factor 4E-binding protein 1
Q6UXG3	1.6474617	0.5118899	9.214163	3.218390	0.0102036	0.0477214	CMRF35-like molecule 9
P03915	-1.1507202	0.3487824	8.365531	-3.299250	0.0102160	0.0477214	NADH-ubiquinone oxidoreductase chain 5
P14174	-0.8418646	0.2604176	8.972480	-3.232749	0.0103183	0.0480721	Macrophage migration inhibitory factor
P34947	-1.4080509	0.4397019	9.309723	-3.202285	0.0103383	0.0480721	G protein-coupled receptor kinase 5
O75436	-0.9929865	0.3057820	8.699459	-3.247368	0.0104998	0.0487005	Vacuolar protein sorting-associated protein 26A
P19474	-1.1365988	0.3407498	7.878639	-3.335581	0.0105265	0.0487005	E3 ubiquitin-protein ligase TRIM21
O14656	-1.8183830	0.5546926	8.368515	-3.278181	0.0105458	0.0487005	Torsin-1A
Q08AG7	-1.1984106	0.3483075	7.109531	-3.440669	0.0105693	0.0487005	Mitotic-spindle organizing protein 1
P05060	-2.3136323	0.6779642	7.262114	-3.412617	0.0106338	0.0488867	Secretogranin-1;PE-11;GAWK peptide;CCB peptide
Q08211	-0.6963521	0.2190460	9.365549	-3.179022	0.0106598	0.0488953	ATP-dependent RNA helicase A
Q0VAK6	1.1733962	0.3600666	8.440932	3.258831	0.0107382	0.0491443	Leiomodin-3
P51665	-0.7816374	0.2456015	9.245677	-3.182543	0.0107697	0.0491777	26S proteasome non-ATPase regulatory subunit 7
Q9H2J4	-0.8248510	0.2601050	9.365549	-3.171223	0.0107971	0.0491799	Phosducin-like protein 3
Q8IWB7	1.6050991	0.4817042	7.757101	3.332126	0.0108186	0.0491799	WD repeat and FYVE domain-containing protein 1
P51970	0.7463947	0.2339250	9.052480	3.190743	0.0109130	0.0494170	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Q15691	-0.9045387	0.2773318	8.310907	-3.261576	0.0109194	0.0494170	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 
##                         0.5564844                         0.6124058 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.4126486                         0.8296480

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,]