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(
  assayData = read.delim(peptidesFile),
  fnames = 1,
  quantCols =  ecols,
  name = "peptideRaw")

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))

## 'Proteins' found in 2 out of 2 assay(s)

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 != "+")

## 'Potential.contaminant' found in 2 out of 2 assay(s)

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)

## 'nNonZero' found in 2 out of 2 assay(s)

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 205 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	0.4386062	9.420359	18.166527	0.0000000	0.0000245	Myosin light chain 3
P12883	4.6698827	0.3735126	9.234880	12.502610	0.0000004	0.0004387	Myosin-7
P10916	6.9261087	0.5305670	7.420359	13.054165	0.0000022	0.0015039	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q6UWY5	-3.2536428	0.3846747	9.166472	-8.458166	0.0000126	0.0050454	Olfactomedin-like protein 1
O75368	-2.2715945	0.2746175	9.342472	-8.271850	0.0000135	0.0050454	SH3 domain-binding glutamic acid-rich-like protein
P46821	-2.1668803	0.2664151	9.420359	-8.133473	0.0000147	0.0050454	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
O95865	-2.1732192	0.2854548	9.420359	-7.613183	0.0000254	0.0066381	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q8N474	-3.3090235	0.3826720	7.950693	-8.647153	0.0000258	0.0066381	Secreted frizzled-related protein 1
Q9ULL5-3	-3.4165405	0.4016851	7.899339	-8.505520	0.0000302	0.0069160	Proline-rich protein 12
P21810	-3.2145420	0.4232686	8.810008	-7.594568	0.0000376	0.0071804	Biglycan
P14854	2.4019126	0.3085593	8.484681	7.784282	0.0000384	0.0071804	Cytochrome c oxidase subunit 6B1
O94875-10	2.3744000	0.3210591	8.958125	7.395523	0.0000423	0.0072492	Sorbin and SH3 domain-containing protein 2
P05546	-1.9318824	0.2730471	9.324873	-7.075271	0.0000486	0.0076991	Heparin cofactor 2
P29622	-2.1134793	0.3039016	9.420359	-6.954485	0.0000530	0.0077940	Kallistatin
Q16647	-2.7991521	0.3979468	9.081456	-7.033986	0.0000582	0.0079891	Prostacyclin synthase
P02452	-2.9630153	0.4018280	8.345480	-7.373839	0.0000628	0.0080762	Collagen alpha-1(I) chain
P51884	-2.1343314	0.3184899	9.210584	-6.701409	0.0000793	0.0095563	Lumican
Q8TBQ9	-2.8189960	0.4079802	8.676104	-6.909640	0.0000836	0.0095563	Protein kish-A
P36955	-2.3377901	0.3380798	8.196767	-6.914907	0.0001093	0.0097605	Pigment epithelium-derived factor
Q9UBG0	-2.5547510	0.3990636	9.225608	-6.401864	0.0001120	0.0097605	C-type mannose receptor 2
P00325	-2.1119462	0.3259838	9.037213	-6.478684	0.0001122	0.0097605	Alcohol dehydrogenase 1B
P07451	-1.8489373	0.2923533	9.420359	-6.324324	0.0001123	0.0097605	Carbonic anhydrase 3
P23083	-4.2325442	0.5743071	7.420359	-7.369827	0.0001148	0.0097605	Ig heavy chain V-I region V35
P24844	-2.4962161	0.3945586	9.365146	-6.326604	0.0001149	0.0097605	Myosin regulatory light polypeptide 9
Q15113	-2.7424988	0.4339863	9.239033	-6.319320	0.0001230	0.0097605	Procollagen C-endopeptidase enhancer 1
P51888	-3.0081810	0.4037624	7.212550	-7.450374	0.0001233	0.0097605	Prolargin
Q06828	-4.2030186	0.6620572	9.022216	-6.348422	0.0001317	0.0099192	Fibromodulin
Q53GQ0	-2.4232423	0.3921550	9.410782	-6.179296	0.0001350	0.0099192	Very-long-chain 3-oxoacyl-CoA reductase
P13533	-4.0404076	0.6480615	9.151585	-6.234605	0.0001420	0.0100740	Myosin-6
P35442	-2.3010500	0.3542666	8.420359	-6.495250	0.0001509	0.0103503	Thrombospondin-2
P08294	-2.7503241	0.4275819	8.014829	-6.432274	0.0002005	0.0131731	Extracellular superoxide dismutase [Cu-Zn]
Q96LL9	-2.4127080	0.4001370	8.810329	-6.029705	0.0002128	0.0131731	DnaJ homolog subfamily C member 30
P36021	-3.1085951	0.5045027	8.420359	-6.161702	0.0002193	0.0131731	Monocarboxylate transporter 8
P18428	-1.9996058	0.3407167	9.191871	-5.868822	0.0002193	0.0131731	Lipopolysaccharide-binding protein
Q9UL18	-2.6225313	0.4111229	7.913528	-6.378947	0.0002240	0.0131731	Protein argonaute-1
Q92508	4.0552373	0.5586150	6.420359	7.259450	0.0002541	0.0145255	Piezo-type mechanosensitive ion channel component 1
P46060	-1.9620904	0.3284336	8.420359	-5.974085	0.0002723	0.0150027	Ran GTPase-activating protein 1
P02743	-2.1700557	0.3863985	9.420359	-5.616108	0.0002772	0.0150027	Serum amyloid P-component;Serum amyloid P-component(1-203)
P05997	-3.0856148	0.5411521	8.993385	-5.701936	0.0002944	0.0150027	Collagen alpha-2(V) chain
Q9UGT4	-2.3006162	0.4092617	9.245036	-5.621381	0.0002949	0.0150027	Sushi domain-containing protein 2
Q14764	-1.6267934	0.2926175	9.420359	-5.559454	0.0002989	0.0150027	Major vault protein
Q8WWA0	-5.8725166	0.9857040	8.156016	-5.957687	0.0003145	0.0151581	Intelectin-1
O60760	-3.5990151	0.6219772	8.420359	-5.786410	0.0003396	0.0151581	Hematopoietic prostaglandin D synthase
O43677	-2.7199107	0.4724234	8.483808	-5.757358	0.0003418	0.0151581	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q9BW30	-2.7245919	0.4899368	9.052429	-5.561109	0.0003441	0.0151581	Tubulin polymerization-promoting protein family member 3
Q9P2B2	-2.0393915	0.3747097	9.420359	-5.442591	0.0003496	0.0151581	Prostaglandin F2 receptor negative regulator
Q9UBB5	2.7451793	0.4000606	6.420359	6.861908	0.0003517	0.0151581	Methyl-CpG-binding domain protein 2
P40261	-2.3445730	0.4282291	9.273912	-5.475044	0.0003535	0.0151581	Nicotinamide N-methyltransferase
Q9NZ01	-2.4109216	0.4375281	8.685989	-5.510325	0.0004252	0.0172070	Very-long-chain enoyl-CoA reductase
P00748	-1.9914680	0.3712703	9.156315	-5.363931	0.0004282	0.0172070	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q92736-2	-3.3064395	0.6042970	8.766703	-5.471547	0.0004323	0.0172070	Ryanodine receptor 2
O14967	-2.3785961	0.4303723	8.580509	-5.526834	0.0004348	0.0172070	Calmegin
O00180	-4.2526703	0.7658995	8.420359	-5.552517	0.0004502	0.0174825	Potassium channel subfamily K member 1
P12110	-1.9881397	0.3554165	8.222232	-5.593831	0.0004662	0.0177279	Collagen alpha-2(VI) chain
Q07954	-1.6573532	0.3175193	9.420359	-5.219693	0.0004738	0.0177279	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
O95980	-2.5277905	0.4569818	8.199718	-5.531490	0.0005071	0.0186373	Reversion-inducing cysteine-rich protein with Kazal motifs
P31994-2	-1.5795166	0.3043264	9.122267	-5.190206	0.0005473	0.0196543	Low affinity immunoglobulin gamma Fc region receptor II-b
O00264	-1.9731043	0.3803391	9.097380	-5.187750	0.0005539	0.0196543	Membrane-associated progesterone receptor component 1
Q14195-2	-2.5380012	0.4966607	9.283388	-5.110131	0.0005775	0.0198432	Dihydropyrimidinase-related protein 3
Q8TBP6	-1.9233155	0.3718274	9.032046	-5.172602	0.0005785	0.0198432	Solute carrier family 25 member 40
Q8WZA9	-1.4960398	0.2943543	9.231251	-5.082446	0.0006106	0.0203049	Immunity-related GTPase family Q protein
Q9BXN1	-2.6634064	0.5185471	9.012323	-5.136287	0.0006117	0.0203049	Asporin
O43464	-1.9028432	0.3769428	9.166698	-5.048095	0.0006542	0.0210534	Serine protease HTRA2, mitochondrial
P01699	-4.3035389	0.6908090	6.301890	-6.229709	0.0006547	0.0210534	Ig lambda chain V-I region VOR
Q9GZY4	-3.1557642	0.5788229	7.775949	-5.452037	0.0006690	0.0211457	Cytochrome c oxidase assembly factor 1 homolog
Q9NVN8	-6.0616246	0.8752359	5.420359	-6.925704	0.0006911	0.0211457	Guanine nucleotide-binding protein-like 3-like protein
P41240	-1.5466953	0.3073684	9.050310	-5.032058	0.0006955	0.0211457	Tyrosine-protein kinase CSK
P06858	1.7891922	0.3600895	9.302479	4.968743	0.0006987	0.0211457	Lipoprotein lipase
O95631	-3.9795086	0.5835987	5.420359	-6.818912	0.0007462	0.0217213	Netrin-1
P04083	-1.5201990	0.3111586	9.420359	-4.885608	0.0007573	0.0217213	Annexin A1
Q8NAT1	-1.3792038	0.2816741	9.360836	-4.896452	0.0007596	0.0217213	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
P02747	-2.6697776	0.4727594	7.043683	-5.647223	0.0007599	0.0217213	Complement C1q subcomponent subunit C
Q92621	-1.7036447	0.3526893	9.417394	-4.830440	0.0008203	0.0227488	Nuclear pore complex protein Nup205
A6NMZ7	-2.2762344	0.4717832	9.420359	-4.824746	0.0008263	0.0227488	Collagen alpha-6(VI) chain
Q9NY15	-2.1436460	0.4441922	9.403688	-4.825943	0.0008290	0.0227488	Stabilin-1
P02775	-1.9622566	0.4084962	9.420359	-4.803610	0.0008518	0.0230658	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)
Q92604	-2.2504519	0.4687530	9.352385	-4.800934	0.0008727	0.0233221	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
Q96C86	-1.4762676	0.3054387	9.149198	-4.833270	0.0008871	0.0233221	m7GpppX diphosphatase
O14980	-1.2169774	0.2551792	9.420359	-4.769109	0.0008953	0.0233221	Exportin-1
P48681	-1.3334013	0.2810861	9.417394	-4.743747	0.0009295	0.0239120	Nestin
Q9UNW9	4.0122337	0.8547106	9.142176	4.694260	0.0010823	0.0268544	RNA-binding protein Nova-2
P24311	1.7937075	0.3882030	9.420359	4.620540	0.0011114	0.0268544	Cytochrome c oxidase subunit 7B, mitochondrial
P50552	-1.5288544	0.3255300	9.036834	-4.696508	0.0011133	0.0268544	Vasodilator-stimulated phosphoprotein
Q53GG5-2	-2.9088697	0.6018399	8.409844	-4.833295	0.0011275	0.0268544	PDZ and LIM domain protein 3
Q7L4S7	-1.7124303	0.3273125	7.153052	-5.231790	0.0011302	0.0268544	Protein ARMCX6
Q8WY22	-1.8091979	0.3749461	8.420359	-4.825221	0.0011356	0.0268544	BRI3-binding protein
P56539	-2.0161968	0.4222161	8.599057	-4.775273	0.0011445	0.0268544	Caveolin-3
P49207	-1.5105253	0.3230060	9.024427	-4.676462	0.0011496	0.0268544	60S ribosomal protein L34
Q5M9N0	-3.5146838	0.7308851	8.385642	-4.808805	0.0011741	0.0268544	Coiled-coil domain-containing protein 158
P46063	-1.3496984	0.2916572	9.183164	-4.627688	0.0011764	0.0268544	ATP-dependent DNA helicase Q1
Q6SZW1	-2.6395602	0.5203026	7.420359	-5.073125	0.0012090	0.0268544	Sterile alpha and TIR motif-containing protein 1
P02671	-2.1346012	0.3881675	6.417394	-5.499175	0.0012144	0.0268544	Fibrinogen alpha chain;Fibrinopeptide A;Fibrinogen alpha chain
Q5NDL2	-2.2948242	0.4886297	8.717721	-4.696449	0.0012273	0.0268544	EGF domain-specific O-linked N-acetylglucosamine transferase
Q9HAV4	-2.4188578	0.4860155	7.670496	-4.976915	0.0012275	0.0268544	Exportin-5
Q9BXR6	-2.3571850	0.5184175	9.417394	-4.546886	0.0012396	0.0268544	Complement factor H-related protein 5
Q92681	-2.1962163	0.4515818	7.932336	-4.863385	0.0012812	0.0274650	Regulatory solute carrier protein family 1 member 1
Q96H79	-3.2031583	0.5775193	6.200924	-5.546409	0.0013005	0.0275566	Zinc finger CCCH-type antiviral protein 1-like
Q8TDB6	-1.7610737	0.3855338	9.102046	-4.567884	0.0013122	0.0275566	E3 ubiquitin-protein ligase DTX3L
O15230	-1.4246624	0.3071116	8.689548	-4.638909	0.0013403	0.0278624	Laminin subunit alpha-5
Q15274	-1.9285076	0.4023627	7.916098	-4.792959	0.0014087	0.0289903	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q9BUF5	-1.9157084	0.4285093	9.301065	-4.470635	0.0014314	0.0290457	Tubulin beta-6 chain
Q9Y5U8	-4.0913780	0.9166412	9.319580	-4.463445	0.0014396	0.0290457	Mitochondrial pyruvate carrier 1
P14550	-1.3982496	0.3076929	8.855961	-4.544302	0.0014562	0.0290948	Alcohol dehydrogenase [NADP(+)]
O15111	-1.9484725	0.3851415	6.956358	-5.059108	0.0014925	0.0295349	Inhibitor of nuclear factor kappa-B kinase subunit alpha
Q12996	-2.0094808	0.3831587	6.493841	-5.244512	0.0015107	0.0296094	Cleavage stimulation factor subunit 3
Q9UBI9	-2.9866384	0.6067195	7.231219	-4.922602	0.0015558	0.0296875	Headcase protein homolog
O75828	-1.6544202	0.3767450	9.420359	-4.391353	0.0015612	0.0296875	Carbonyl reductase [NADPH] 3
P06727	-1.3683135	0.3043718	8.840955	-4.495533	0.0015671	0.0296875	Apolipoprotein A-IV
P04196	-1.9303128	0.4001227	7.506343	-4.824303	0.0015724	0.0296875	Histidine-rich glycoprotein
Q9ULC3	-1.6333020	0.3645496	8.720682	-4.480329	0.0016570	0.0309524	Ras-related protein Rab-23
P14555	-4.6109150	0.9289708	6.916563	-4.963466	0.0016891	0.0309524	Phospholipase A2, membrane associated
P02461	-3.6062939	0.7964105	8.416773	-4.528185	0.0016954	0.0309524	Collagen alpha-1(III) chain
Q6ZSY5	-1.6890696	0.3871892	9.235896	-4.362389	0.0017089	0.0309524	Protein phosphatase 1 regulatory subunit 3F
P01031	-1.3157564	0.2928900	8.544930	-4.492322	0.0017146	0.0309524	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q8N5M1	-1.9899041	0.4567857	9.122947	-4.356319	0.0017753	0.0317701	ATP synthase mitochondrial F1 complex assembly factor 2
P04003	-1.5009188	0.3436224	9.023047	-4.367931	0.0017916	0.0317849	C4b-binding protein alpha chain
P45877	-1.2442932	0.2899715	9.420359	-4.291088	0.0018158	0.0319386	Peptidyl-prolyl cis-trans isomerase C
P08582	-1.6911943	0.3948150	9.394818	-4.283511	0.0018482	0.0322331	Melanotransferrin
Q6YN16	1.5603531	0.3657250	9.420359	4.266465	0.0018848	0.0325586	Hydroxysteroid dehydrogenase-like protein 2
Q13636	-3.2633858	0.6344956	6.233646	-5.143276	0.0018985	0.0325586	Ras-related protein Rab-31
O75746	-1.5795706	0.3608149	8.652741	-4.377787	0.0019522	0.0332039	Calcium-binding mitochondrial carrier protein Aralar1
Q9UQ35	-1.3570787	0.3202712	9.401099	-4.237279	0.0019793	0.0332620	Serine/arginine repetitive matrix protein 2
P34932	-1.1578310	0.2723151	9.291753	-4.251806	0.0019880	0.0332620	Heat shock 70 kDa protein 4
Q5VIR6-4	-1.7638024	0.4142915	9.167220	-4.257395	0.0020325	0.0336262	Vacuolar protein sorting-associated protein 53 homolog
P04004	-1.6269790	0.3774162	8.785099	-4.310835	0.0020725	0.0336262	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P01042	-2.2103015	0.4751169	7.306380	-4.652122	0.0020862	0.0336262	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
P02776	-1.7615098	0.3949258	8.029185	-4.460356	0.0020911	0.0336262	Platelet factor 4;Platelet factor 4, short form
Q9H1E5	-1.3852786	0.3303392	9.420359	-4.193504	0.0021061	0.0336262	Thioredoxin-related transmembrane protein 4
Q8WWQ0	-1.6224614	0.3871144	9.420359	-4.191168	0.0021137	0.0336262	PH-interacting protein
P04209	1.3436120	0.3180816	9.190380	4.224111	0.0021241	0.0336262	Ig lambda chain V-II region NIG-84
P15924	1.2648885	0.3029535	9.383746	4.175190	0.0021844	0.0343167	Desmoplakin
Q9BTV4	-1.8099873	0.4323541	9.211817	-4.186353	0.0022365	0.0344787	Transmembrane protein 43
Q08945	-2.0204841	0.4675424	8.420359	-4.321499	0.0022538	0.0344787	FACT complex subunit SSRP1
Q2TAA5	-1.2916274	0.3093292	9.234456	-4.175575	0.0022609	0.0344787	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
Q53T59	-1.8461756	0.4200861	8.037638	-4.394755	0.0022769	0.0344787	HCLS1-binding protein 3
Q04721	1.5358466	0.3685976	9.213519	4.166730	0.0023027	0.0344787	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
P09619	-1.6085799	0.3866754	9.226613	-4.160027	0.0023189	0.0344787	Platelet-derived growth factor receptor beta
Q5JPH6	3.5281305	0.6863030	5.829289	5.140777	0.0023262	0.0344787	Probable glutamate–tRNA ligase, mitochondrial
P05455	-1.2004499	0.2883779	9.171164	-4.162767	0.0023398	0.0344787	Lupus La protein
Q9Y6X5	-1.3875045	0.3272759	8.705094	-4.239556	0.0023455	0.0344787	Bis(5-adenosyl)-triphosphatase ENPP4
O60262	-1.5577722	0.3689381	8.700017	-4.222313	0.0024077	0.0351428	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
O75348	-1.8591253	0.4535299	9.420359	-4.099234	0.0024337	0.0352720	V-type proton ATPase subunit G 1
O00303	-1.4561773	0.3518679	9.051187	-4.138420	0.0024969	0.0359346	Eukaryotic translation initiation factor 3 subunit F
P01034	-1.6978634	0.4087932	8.859133	-4.153355	0.0025581	0.0365590	Cystatin-C
P49458	-2.2735269	0.5075335	7.251835	-4.479560	0.0026268	0.0372073	Signal recognition particle 9 kDa protein
P25940	-1.7454125	0.4272441	9.155619	-4.085281	0.0026396	0.0372073	Collagen alpha-3(V) chain
P62760	-1.9146688	0.4707491	9.159766	-4.067281	0.0027100	0.0379401	Visinin-like protein 1
Q14019	-3.9129083	0.8333648	6.420359	-4.695313	0.0027954	0.0388713	Coactosin-like protein
O15116	-3.2231772	0.6507124	5.794630	-4.953305	0.0028355	0.0391643	U6 snRNA-associated Sm-like protein LSm1
Q9UKS6	1.4372286	0.3556788	8.991910	4.040805	0.0029305	0.0398449	Protein kinase C and casein kinase substrate in neurons protein 3
P08311	-1.3139510	0.3238932	8.882238	-4.056741	0.0029350	0.0398449	Cathepsin G
Q9UKX3	2.1517579	0.5377017	9.238422	4.001769	0.0029429	0.0398449	Myosin-13
P30405	-1.5177122	0.3822973	9.420359	-3.969979	0.0029732	0.0399918	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
P36551	-1.3202398	0.3291895	9.078769	-4.010577	0.0030076	0.0401444	Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial
Q9Y2Z0	-1.7414076	0.4398381	9.420359	-3.959201	0.0030235	0.0401444	Suppressor of G2 allele of SKP1 homolog
P19429	2.3063639	0.5572199	8.211191	4.139056	0.0030787	0.0406150	Troponin I, cardiac muscle
P54577	-1.3002728	0.3261820	9.016679	-3.986341	0.0031635	0.0414677	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
P54652	-1.5932853	0.4025031	9.131756	-3.958443	0.0032184	0.0419203	Heat shock-related 70 kDa protein 2
O75475	-1.9038879	0.4846934	9.293000	-3.928025	0.0032591	0.0421839	PC4 and SFRS1-interacting protein
Q7LBR1	-2.8413335	0.7311661	9.420359	-3.886030	0.0033900	0.0434941	Charged multivesicular body protein 1b
P25311	-1.5051007	0.3754727	8.556242	-4.008549	0.0034026	0.0434941	Zinc-alpha-2-glycoprotein
P60468	-1.4647431	0.3625247	8.275558	-4.040396	0.0034805	0.0442150	Protein transport protein Sec61 subunit beta
Q04941	-1.9356392	0.4958892	9.122186	-3.903371	0.0035088	0.0443012	Proteolipid protein 2
Q9BS26	-1.2463986	0.3225161	9.354832	-3.864609	0.0035522	0.0443625	Endoplasmic reticulum resident protein 44
P03950	-2.2030636	0.5456390	8.205145	-4.037585	0.0035568	0.0443625	Angiogenin
Q13641	-2.2297004	0.5236478	7.111870	-4.258015	0.0036223	0.0449080	Trophoblast glycoprotein
Q1KMD3	-1.4744120	0.3796403	9.065422	-3.883707	0.0036596	0.0450983	Heterogeneous nuclear ribonucleoprotein U-like protein 2
P26447	-1.8372154	0.4683842	8.758554	-3.922454	0.0036879	0.0451764	Protein S100-A4
Q96PK6	-1.3089284	0.3399205	9.118686	-3.850690	0.0038077	0.0461431	RNA-binding protein 14
O00567	-2.4335450	0.6369246	9.345669	-3.820774	0.0038116	0.0461431	Nucleolar protein 56
P12814	-1.6827515	0.4236455	8.209855	-3.972075	0.0038987	0.0465538	Alpha-actinin-1
Q9Y3B4	-1.2603707	0.3283823	9.068421	-3.838121	0.0039223	0.0465538	Splicing factor 3B subunit 6
Q86VU5	1.5583619	0.4110443	9.420359	3.791226	0.0039358	0.0465538	Catechol O-methyltransferase domain-containing protein 1
Q13478	-1.6083281	0.4182581	8.998109	-3.845301	0.0039360	0.0465538	Interleukin-18 receptor 1
Q9HB40	-2.1393191	0.4860845	6.361260	-4.401126	0.0039678	0.0466612	Retinoid-inducible serine carboxypeptidase
P01024	-1.1180307	0.2936124	9.157785	-3.807846	0.0040365	0.0469892	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
P01008	-1.5692162	0.4151767	9.376569	-3.779635	0.0040423	0.0469892	Antithrombin-III
P07384	-1.1052065	0.2922209	9.301416	-3.782093	0.0040852	0.0469892	Calpain-1 catalytic subunit
P14543	-1.4365423	0.3779966	9.153301	-3.800411	0.0040870	0.0469892	Nidogen-1
Q14011	-2.3803571	0.6080384	8.287145	-3.914814	0.0041543	0.0469943	Cold-inducible RNA-binding protein
Q9UK22	-1.8807802	0.4332817	6.412167	-4.340779	0.0041699	0.0469943	F-box only protein 2
Q7Z3T8	-1.6269924	0.4212289	8.586144	-3.862490	0.0041889	0.0469943	Zinc finger FYVE domain-containing protein 16
O95486	-1.7001274	0.4483551	9.078202	-3.791922	0.0042035	0.0469943	Protein transport protein Sec24A
O94919	-1.1247209	0.2979363	9.184104	-3.775038	0.0042258	0.0469943	Endonuclease domain-containing 1 protein
Q9Y2D4	-2.0300937	0.5292407	8.722544	-3.835861	0.0042314	0.0469943	Exocyst complex component 6B
Q9BXY0	-1.9170100	0.4391665	6.280367	-4.365109	0.0042597	0.0469943	Protein MAK16 homolog
P07357	-1.1425305	0.3041753	9.262894	-3.756158	0.0042866	0.0469943	Complement component C8 alpha chain
Q96ST3	-1.6077298	0.4259265	9.106665	-3.774665	0.0042930	0.0469943	Paired amphipathic helix protein Sin3a
P09467	-2.0219103	0.4961051	7.273827	-4.075568	0.0043480	0.0473449	Fructose-1,6-bisphosphatase 1
Q9BVC6	-1.6329609	0.4385611	9.420359	-3.723452	0.0043822	0.0473476	Transmembrane protein 109
P56199	-1.2716373	0.3331933	8.643688	-3.816515	0.0044299	0.0473476	Integrin alpha-1
P50991	-1.7929240	0.4666148	8.464244	-3.842407	0.0044330	0.0473476	T-complex protein 1 subunit delta
P51665	-1.2958979	0.3474655	9.297522	-3.729573	0.0044403	0.0473476	26S proteasome non-ATPase regulatory subunit 7
Q6IC98	-1.1710653	0.3080453	8.655845	-3.801601	0.0045182	0.0478405	GRAM domain-containing protein 4
O43143	-0.9916403	0.2678535	9.420359	-3.702173	0.0045330	0.0478405	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
Q6ZWT7	-2.6237461	0.5678695	5.420359	-4.620333	0.0046816	0.0489641	Lysophospholipid acyltransferase 2
Q96FJ2	1.5408850	0.4077907	8.645240	3.778617	0.0046870	0.0489641	Dynein light chain 2, cytoplasmic
Q6P587	5.5394450	1.3247288	6.582444	4.181569	0.0047308	0.0491316	Acylpyruvase FAHD1, mitochondrial
P04843	-2.0344244	0.5402204	8.671925	-3.765915	0.0047508	0.0491316	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
Q53FA7	1.8348852	0.4967783	9.200370	3.693570	0.0047852	0.0492400	Quinone oxidoreductase PIG3
P23434	1.1390966	0.3110180	9.420359	3.662478	0.0048291	0.0493121	Glycine cleavage system H protein, mitochondrial
Q6P1N0	-1.7290768	0.4259682	6.982437	-4.059169	0.0048402	0.0493121	Coiled-coil and C2 domain-containing protein 1A
Q8NBF2	-1.1613746	0.3170052	9.347444	-3.663582	0.0048840	0.0495134	NHL repeat-containing protein 2
A8MTT3	-3.4393264	0.8546736	7.072356	-4.024140	0.0049270	0.0497049	Protein CEBPZOS
P80723	-1.6306847	0.4256214	8.027411	-3.831303	0.0049765	0.0499596	Brain acid soluble protein 1

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	0.4386062	9.420359	12.548473	0.0000003	0.0006953	Myosin light chain 3
P06858	3.354674	0.3563885	9.302479	9.412969	0.0000047	0.0047476	Lipoprotein lipase
Q9ULD0	-3.575906	0.3771803	7.420359	-9.480629	0.0000208	0.0141249	2-oxoglutarate dehydrogenase-like, mitochondrial
P35442	-3.246460	0.4090718	8.420359	-7.936162	0.0000346	0.0148139	Thrombospondin-2
P02776	-2.818363	0.3445433	8.029185	-8.179999	0.0000364	0.0148139	Platelet factor 4;Platelet factor 4, short form
P21810	-2.924783	0.4096541	8.810008	-7.139639	0.0000605	0.0199120	Biglycan
O75368	-1.819326	0.2727814	9.342472	-6.669538	0.0000769	0.0199120	SH3 domain-binding glutamic acid-rich-like protein
A6NMZ7	-3.070848	0.4717832	9.420359	-6.509023	0.0000897	0.0199120	Collagen alpha-6(VI) chain
P54652	-2.726681	0.4132258	9.131756	-6.598526	0.0000930	0.0199120	Heat shock-related 70 kDa protein 2
Q6UWY5	-2.456874	0.3756784	9.166472	-6.539833	0.0000979	0.0199120	Olfactomedin-like protein 1
Q06828	-4.122091	0.6362258	9.022216	-6.478974	0.0001130	0.0208866	Fibromodulin
P05546	-1.727800	0.2753193	9.324873	-6.275623	0.0001246	0.0211179	Heparin cofactor 2
P28066	-2.176824	0.3408032	8.782994	-6.387335	0.0001415	0.0212787	Proteasome subunit alpha type-5
P29622	-1.847919	0.3039016	9.420359	-6.080651	0.0001521	0.0212787	Kallistatin
P46821	-1.606539	0.2664151	9.420359	-6.030208	0.0001621	0.0212787	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P13533	-3.888317	0.6374638	9.151585	-6.099666	0.0001674	0.0212787	Myosin-6
Q9UGT4	-2.443145	0.4157640	9.245036	-5.876278	0.0002124	0.0240607	Sushi domain-containing protein 2
P35625	-3.938312	0.6166712	7.993494	-6.386405	0.0002129	0.0240607	Metalloproteinase inhibitor 3
Q69YU5	3.254738	0.5563163	8.748634	5.850517	0.0002718	0.0263699	Uncharacterized protein C12orf73
Q6PCB0	-2.328852	0.4050843	8.987253	-5.749055	0.0002781	0.0263699	von Willebrand factor A domain-containing protein 1
O43677	-2.969964	0.5074118	8.483808	-5.853162	0.0003049	0.0263699	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q15327	-2.203003	0.3952242	9.289627	-5.574058	0.0003083	0.0263699	Ankyrin repeat domain-containing protein 1
P60468	-2.438022	0.4136717	8.275558	-5.893616	0.0003199	0.0263699	Protein transport protein Sec61 subunit beta
Q14764	-1.608232	0.2926175	9.420359	-5.496021	0.0003253	0.0263699	Major vault protein
P01031	-1.626524	0.2847080	8.544930	-5.712955	0.0003512	0.0263699	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q9P2B2	-2.035226	0.3747097	9.420359	-5.431474	0.0003548	0.0263699	Prostaglandin F2 receptor negative regulator
Q92930	-2.833666	0.4683580	7.661957	-6.050213	0.0003628	0.0263699	Ras-related protein Rab-8B
P02775	-2.205543	0.4084962	9.420359	-5.399176	0.0003707	0.0263699	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	0.4904610	7.625022	-6.034587	0.0003760	0.0263699	NADP-dependent malic enzyme
P12883	1.969100	0.3673074	9.234880	5.360905	0.0004177	0.0277097	Myosin-7
P48681	-1.491288	0.2811556	9.417394	-5.304137	0.0004223	0.0277097	Nestin
P11586	2.013301	0.3551466	8.048875	5.668929	0.0004607	0.0292833	C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
P30711	-2.321740	0.4494189	9.090577	-5.166094	0.0005717	0.0337808	Glutathione S-transferase theta-1
Q9BZH6	3.442805	0.6418925	8.373591	5.363523	0.0005792	0.0337808	WD repeat-containing protein 11
Q9UHG2	-3.175806	0.6110813	8.897312	-5.197026	0.0005876	0.0337808	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
Q9H1K0	-2.237374	0.3926326	7.420359	-5.698390	0.0005979	0.0337808	Rabenosyn-5
P00748	-1.915326	0.3805658	9.156315	-5.032839	0.0006705	0.0352687	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q5NDL2	-2.708130	0.5263639	8.717721	-5.144976	0.0006715	0.0352687	EGF domain-specific O-linked N-acetylglucosamine transferase
O00180	-4.621308	0.8843846	8.420359	-5.225451	0.0006762	0.0352687	Potassium channel subfamily K member 1
P23142	-2.779235	0.5096807	7.589046	-5.452894	0.0007260	0.0355824	Fibulin-1
P10916	2.921175	0.5305670	7.420359	5.505761	0.0007386	0.0355824	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q00G26	1.964123	0.3627114	7.603807	5.415112	0.0007530	0.0355824	Perilipin-5
Q09161	2.370716	0.3907735	6.213723	6.066728	0.0007988	0.0355824	Nuclear cap-binding protein subunit 1
Q9BW30	-2.326597	0.4732990	9.052429	-4.915702	0.0008155	0.0355824	Tubulin polymerization-promoting protein family member 3
Q5JPH6	3.287773	0.5205786	5.829289	6.315614	0.0008229	0.0355824	Probable glutamate–tRNA ligase, mitochondrial
P30405	-1.842938	0.3822973	9.420359	-4.820693	0.0008311	0.0355824	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
P18428	-1.690875	0.3476064	9.191871	-4.864339	0.0008380	0.0355824	Lipopolysaccharide-binding protein
Q9NRG4	2.622493	0.5186766	8.420359	5.056124	0.0008397	0.0355824	N-lysine methyltransferase SMYD2
Q9BUH6	-1.485484	0.3091856	9.196292	-4.804507	0.0009105	0.0376245	Protein PAXX
P35052	-1.965366	0.3813736	7.847326	-5.153388	0.0009249	0.0376245	Glypican-1;Secreted glypican-1
O15061	-1.710970	0.3622447	9.420359	-4.723242	0.0009567	0.0381573	Synemin
P08603	-1.484314	0.3171820	9.420359	-4.679692	0.0010193	0.0390854	Complement factor H
Q96FN9	-2.712489	0.5555777	8.420359	-4.882287	0.0010532	0.0390854	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
Q04760	2.254328	0.4719185	8.783089	4.776944	0.0010764	0.0390854	Lactoylglutathione lyase
Q96KC8	-2.480944	0.5072249	8.308217	-4.891212	0.0010821	0.0390854	DnaJ homolog subfamily C member 1
Q99983	-3.527403	0.6599123	6.949931	-5.345260	0.0010949	0.0390854	Osteomodulin
Q8N474	-2.108536	0.4231404	7.950693	-4.983065	0.0010953	0.0390854	Secreted frizzled-related protein 1
P04004	-1.908509	0.4017669	8.785099	-4.750289	0.0011159	0.0391329	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P24298	1.991397	0.4203117	8.641195	4.737905	0.0011878	0.0409503	Alanine aminotransferase 1
P62857	-2.074531	0.4177502	7.713404	-4.965961	0.0012237	0.0414819	40S ribosomal protein S28
P23434	1.406476	0.3110180	9.420359	4.522170	0.0012847	0.0428390	Glycine cleavage system H protein, mitochondrial
P24844	-1.767461	0.3927048	9.365146	-4.500736	0.0013459	0.0441553	Myosin regulatory light polypeptide 9
Q6PI78	1.975693	0.4394104	9.092174	4.496236	0.0014592	0.0453981	Transmembrane protein 65
Q15113	-1.959899	0.4411390	9.239033	-4.442814	0.0015161	0.0453981	Procollagen C-endopeptidase enhancer 1
P04275	-1.352764	0.3015061	8.996018	-4.486688	0.0015194	0.0453981	von Willebrand factor;von Willebrand antigen 2
P01611	-2.213481	0.5026161	9.420359	-4.403920	0.0015321	0.0453981	Ig kappa chain V-I region Wes
P04350	-2.861432	0.5740170	6.993038	-4.984925	0.0015968	0.0453981	Tubulin beta-4A chain
Q9BSD7	2.993219	0.6098849	7.206934	4.907844	0.0015982	0.0453981	Cancer-related nucleoside-triphosphatase
Q86WV6	-1.310297	0.2989446	9.275839	-4.383075	0.0016403	0.0453981	Stimulator of interferon genes protein
P51888	-1.838614	0.3767487	7.212550	-4.880213	0.0016469	0.0453981	Prolargin
Q6UWS5	1.798858	0.3707513	7.292033	4.851926	0.0016505	0.0453981	Protein PET117 homolog, mitochondrial
P08294	-1.884866	0.4063094	8.014829	-4.638993	0.0016602	0.0453981	Extracellular superoxide dismutase [Cu-Zn]
Q9UL26	7.763006	1.7464060	8.874918	4.445132	0.0016679	0.0453981	Ras-related protein Rab-22A
Q7L4S7	-2.514619	0.5153140	7.153052	-4.879781	0.0016871	0.0453981	Protein ARMCX6
P01303	-2.151374	0.4876274	8.990424	-4.411922	0.0016952	0.0453981	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
P82663	-1.944516	0.4476294	9.372918	-4.344030	0.0016963	0.0453981	28S ribosomal protein S25, mitochondrial
P50453	-1.398216	0.3190416	8.998589	-4.382552	0.0017652	0.0465364	Serpin B9
Q9HCB6	-2.412515	0.5446307	8.694096	-4.429636	0.0017933	0.0465364	Spondin-1
Q8TDB4	-2.849906	0.5515757	6.286039	-5.166844	0.0018075	0.0465364	Protein MGARP
Q9Y6X5	-1.531154	0.3489548	8.705094	-4.387829	0.0018970	0.0472687	Bis(5-adenosyl)-triphosphatase ENPP4
Q15274	-2.142900	0.4702421	7.916098	-4.557015	0.0019081	0.0472687	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
P02452	-1.816507	0.4086422	8.345480	-4.445226	0.0019402	0.0472687	Collagen alpha-1(I) chain
Q6YN16	1.553070	0.3657250	9.420359	4.246550	0.0019426	0.0472687	Hydroxysteroid dehydrogenase-like protein 2
P61925	2.031117	0.4388273	7.546436	4.628512	0.0019722	0.0472687	cAMP-dependent protein kinase inhibitor alpha
P51884	-1.386041	0.3246504	9.210584	-4.269336	0.0019753	0.0472687	Lumican
P07360	-1.535545	0.3560274	8.758820	-4.312997	0.0020806	0.0492078	Complement component C8 gamma chain
Q96MM6	3.209344	0.6644094	6.744197	4.830370	0.0021064	0.0492466	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 445 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	0.3101414	9.420359	21.718785	0.0000000	0.0000047	Myosin light chain 3
P12883	3.3194914	0.2619286	9.234880	12.673268	0.0000004	0.0003850	Myosin-7
O75368	-2.0454601	0.1935358	9.342472	-10.568898	0.0000017	0.0007252	SH3 domain-binding glutamic acid-rich-like protein
P10916	4.9236420	0.3670984	7.420359	13.412320	0.0000018	0.0007252	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q6UWY5	-2.8552584	0.2688443	9.166472	-10.620493	0.0000019	0.0007252	Olfactomedin-like protein 1
P06858	2.5719330	0.2533166	9.302479	10.153038	0.0000024	0.0007252	Lipoprotein lipase
P46821	-1.8867094	0.1883840	9.420359	-10.015234	0.0000025	0.0007252	Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P21810	-3.0696624	0.2942265	8.810008	-10.432991	0.0000030	0.0007545	Biglycan
P05546	-1.8298412	0.1938785	9.324873	-9.438084	0.0000045	0.0009443	Heparin cofactor 2
P35442	-2.7737551	0.2705756	8.420359	-10.251313	0.0000048	0.0009443	Thrombospondin-2
P29622	-1.9806994	0.2148909	9.420359	-9.217233	0.0000051	0.0009443	Kallistatin
Q06828	-4.1625547	0.4591032	9.022216	-9.066708	0.0000079	0.0013397	Fibromodulin
P13533	-3.9643622	0.4544441	9.151585	-8.723543	0.0000099	0.0015451	Myosin-6
Q8N474	-2.7087798	0.2838348	7.950693	-9.543507	0.0000125	0.0018211	Secreted frizzled-related protein 1
Q9UGT4	-2.3718806	0.2916997	9.245036	-8.131241	0.0000165	0.0020115	Sushi domain-containing protein 2
A6NMZ7	-2.6735410	0.3336011	9.420359	-8.014185	0.0000166	0.0020115	Collagen alpha-6(VI) chain
O95865	-1.5898713	0.2018470	9.420359	-7.876616	0.0000192	0.0020115	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q14764	-1.6175126	0.2069118	9.420359	-7.817401	0.0000204	0.0020115	Major vault protein
O94875-10	1.8826268	0.2322736	8.958125	8.105213	0.0000205	0.0020115	Sorbin and SH3 domain-containing protein 2
P02776	-2.2899367	0.2620479	8.029185	-8.738618	0.0000225	0.0020115	Platelet factor 4;Platelet factor 4, short form
Q9P2B2	-2.0373086	0.2649598	9.420359	-7.689125	0.0000234	0.0020115	Prostaglandin F2 receptor negative regulator
P02452	-2.3897612	0.2863853	8.345480	-8.344567	0.0000250	0.0020115	Collagen alpha-1(I) chain
P24844	-2.1318385	0.2783404	9.365146	-7.659105	0.0000250	0.0020115	Myosin regulatory light polypeptide 9
P51884	-1.7601864	0.2273949	9.210584	-7.740660	0.0000252	0.0020115	Lumican
O43677	-2.8449373	0.3464798	8.483808	-8.210977	0.0000256	0.0020115	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q16647	-2.1622988	0.2772049	9.081456	-7.800362	0.0000257	0.0020115	Prostacyclin synthase
Q15113	-2.3511987	0.3094139	9.239033	-7.598880	0.0000288	0.0021691	Procollagen C-endopeptidase enhancer 1
P18428	-1.8452405	0.2433686	9.191871	-7.582080	0.0000302	0.0021908	Lipopolysaccharide-binding protein
P54652	-2.1599833	0.2884317	9.131756	-7.488717	0.0000345	0.0024215	Heat shock-related 70 kDa protein 2
Q9BW30	-2.5255943	0.3406061	9.052429	-7.415001	0.0000391	0.0024386	Tubulin polymerization-promoting protein family member 3
P02775	-2.0838997	0.2888504	9.420359	-7.214459	0.0000394	0.0024386	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)
P51888	-2.4233975	0.2735767	7.212550	-8.858200	0.0000395	0.0024386	Prolargin
P00748	-1.9533971	0.2658345	9.156315	-7.348170	0.0000396	0.0024386	Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
P48681	-1.4123446	0.1987824	9.417394	-7.104976	0.0000447	0.0026746	Nestin
P08294	-2.3175953	0.2941689	8.014829	-7.878450	0.0000482	0.0027138	Extracellular superoxide dismutase [Cu-Zn]
O00180	-4.4369891	0.5849654	8.420359	-7.585045	0.0000486	0.0027138	Potassium channel subfamily K member 1
P14854	1.7251878	0.2291779	8.484681	7.527724	0.0000494	0.0027138	Cytochrome c oxidase subunit 6B1
P02743	-1.8823835	0.2732250	9.420359	-6.889500	0.0000572	0.0030595	Serum amyloid P-component;Serum amyloid P-component(1-203)
P01031	-1.4711401	0.2044978	8.544930	-7.193917	0.0000667	0.0034811	Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q5NDL2	-2.5014769	0.3591023	8.717721	-6.965916	0.0000768	0.0038819	EGF domain-specific O-linked N-acetylglucosamine transferase
Q92508	3.5430878	0.3997885	6.420359	8.862405	0.0000782	0.0038819	Piezo-type mechanosensitive ion channel component 1
Q53GQ0	-1.8169289	0.2774067	9.410782	-6.549695	0.0000858	0.0040140	Very-long-chain 3-oxoacyl-CoA reductase
P05997	-2.5486728	0.3787258	8.993385	-6.729598	0.0000859	0.0040140	Collagen alpha-2(V) chain
P23083	-3.2601200	0.4241539	7.420359	-7.686172	0.0000868	0.0040140	Ig heavy chain V-I region V35
P60468	-1.9513827	0.2760385	8.275558	-7.069240	0.0000891	0.0040256	Protein transport protein Sec61 subunit beta
Q9ULL5-3	-2.3006667	0.3165385	7.899339	-7.268205	0.0000922	0.0040772	Proline-rich protein 12
Q8TBP6	-1.7084465	0.2583618	9.032046	-6.612613	0.0000963	0.0041153	Solute carrier family 25 member 40
P28066	-1.6712466	0.2493234	8.782994	-6.703127	0.0000989	0.0041153	Proteasome subunit alpha type-5
P35625	-2.9679404	0.4160946	7.993494	-7.132850	0.0000991	0.0041153	Metalloproteinase inhibitor 3
Q14195-2	-2.2534620	0.3490857	9.283388	-6.455327	0.0001022	0.0041571	Dihydropyrimidinase-related protein 3
P46060	-1.7047689	0.2508453	8.420359	-6.796096	0.0001089	0.0043393	Ran GTPase-activating protein 1
Q15327	-1.7740861	0.2778695	9.289627	-6.384601	0.0001109	0.0043393	Ankyrin repeat domain-containing protein 1
Q69YU5	2.5059630	0.3818797	8.748634	6.562178	0.0001180	0.0044197	Uncharacterized protein C12orf73
Q6PCB0	-1.8163629	0.2815416	8.987253	-6.451490	0.0001187	0.0044197	von Willebrand factor A domain-containing protein 1
Q9ULD0	-2.0406330	0.2785661	7.420359	-7.325489	0.0001195	0.0044197	2-oxoglutarate dehydrogenase-like, mitochondrial
P00325	-1.5034066	0.2347510	9.037213	-6.404261	0.0001224	0.0044456	Alcohol dehydrogenase 1B
Q92604	-2.0782169	0.3324288	9.352385	-6.251615	0.0001267	0.0044705	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
P30405	-1.6803249	0.2703250	9.420359	-6.215944	0.0001284	0.0044705	Peptidyl-prolyl cis-trans isomerase F, mitochondrial
P07451	-1.2833190	0.2067250	9.420359	-6.207855	0.0001297	0.0044705	Carbonic anhydrase 3
O14980	-1.1146843	0.1804389	9.420359	-6.177626	0.0001347	0.0045648	Exportin-1
P04004	-1.7677440	0.2756173	8.785099	-6.413763	0.0001371	0.0045725	Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P36955	-1.6933164	0.2541075	8.196767	-6.663779	0.0001420	0.0046576	Pigment epithelium-derived factor
P41240	-1.3344948	0.2135594	9.050310	-6.248821	0.0001463	0.0047120	Tyrosine-protein kinase CSK
P04083	-1.3421955	0.2200224	9.420359	-6.100269	0.0001484	0.0047120	Annexin A1
P36021	-2.5034435	0.3853203	8.420359	-6.497046	0.0001506	0.0047120	Monocarboxylate transporter 8
Q6YN16	1.5567113	0.2586066	9.420359	6.019611	0.0001643	0.0050632	Hydroxysteroid dehydrogenase-like protein 2
Q8WWA0	-4.4529908	0.6836913	8.156016	-6.513160	0.0001704	0.0051332	Intelectin-1
Q8TBQ9	-1.7482778	0.2790057	8.676104	-6.266100	0.0001716	0.0051332	Protein kish-A
Q9BXN1	-2.2858485	0.3741823	9.012323	-6.108916	0.0001763	0.0051428	Asporin
Q15274	-2.0357040	0.3082978	7.916098	-6.603044	0.0001770	0.0051428	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
P04003	-1.4359842	0.2384230	9.023047	-6.022843	0.0001949	0.0055831	C4b-binding protein alpha chain
Q7L4S7	-2.1135247	0.3052384	7.153052	-6.924177	0.0002050	0.0056579	Protein ARMCX6
Q9Y6X5	-1.4593292	0.2392065	8.705094	-6.100710	0.0002053	0.0056579	Bis(5-adenosyl)-triphosphatase ENPP4
O15230	-1.3744676	0.2251448	8.689548	-6.104816	0.0002058	0.0056579	Laminin subunit alpha-5
P14550	-1.3048277	0.2179290	8.855961	-5.987399	0.0002194	0.0058498	Alcohol dehydrogenase [NADP(+)]
P23434	1.2727864	0.2199230	9.420359	5.787420	0.0002214	0.0058498	Glycine cleavage system H protein, mitochondrial
Q9UBG0	-1.6345146	0.2797211	9.225608	-5.843373	0.0002233	0.0058498	C-type mannose receptor 2
Q07954	-1.2959588	0.2245200	9.420359	-5.772130	0.0002259	0.0058498	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
Q9BUF5	-1.7682813	0.3045992	9.301065	-5.805272	0.0002272	0.0058498	Tubulin beta-6 chain
P49207	-1.3710319	0.2330504	9.024427	-5.882985	0.0002315	0.0058858	60S ribosomal protein L34
P23142	-2.2973847	0.3530386	7.589046	-6.507461	0.0002348	0.0058969	Fibulin-1
P04196	-1.6877176	0.2593507	7.506343	-6.507472	0.0002462	0.0061031	Histidine-rich glycoprotein
Q9NRG4	2.3970480	0.3961458	8.420359	6.050924	0.0002490	0.0061031	N-lysine methyltransferase SMYD2
Q9NZ01	-1.8635396	0.3150317	8.685989	-5.915403	0.0002583	0.0062151	Very-long-chain enoyl-CoA reductase
O95980	-1.9294212	0.3158816	8.199718	-6.108051	0.0002597	0.0062151	Reversion-inducing cysteine-rich protein with Kazal motifs
P12110	-1.5935296	0.2644458	8.222232	-6.025921	0.0002819	0.0065643	Collagen alpha-2(VI) chain
P04275	-1.1968998	0.2087610	8.996018	-5.733349	0.0002826	0.0065643	von Willebrand factor;von Willebrand antigen 2
O75828	-1.4912698	0.2663989	9.420359	-5.597882	0.0002840	0.0065643	Carbonyl reductase [NADPH] 3
Q9BZH6	2.6654497	0.4489766	8.373591	5.936723	0.0002907	0.0066332	WD repeat-containing protein 11
Q5JPH6	3.4079519	0.4438849	5.829289	7.677558	0.0002935	0.0066332	Probable glutamate–tRNA ligase, mitochondrial
P07357	-1.1909118	0.2136116	9.262894	-5.575127	0.0003111	0.0069535	Complement component C8 alpha chain
P24298	1.6449487	0.2854239	8.641195	5.763178	0.0003168	0.0070046	Alanine aminotransferase 1
Q86WV6	-1.1787564	0.2127534	9.275839	-5.540483	0.0003240	0.0070857	Stimulator of interferon genes protein
P62760	-1.8748180	0.3370001	9.159766	-5.563257	0.0003290	0.0071182	Visinin-like protein 1
P30711	-1.7974916	0.3228953	9.090577	-5.566793	0.0003365	0.0071979	Glutathione S-transferase theta-1
Q9UHG2	-2.3658698	0.4209729	8.897312	-5.620006	0.0003397	0.0071979	ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
Q92681	-1.8052155	0.3030168	7.932336	-5.957477	0.0003505	0.0073112	Regulatory solute carrier protein family 1 member 1
P01024	-1.1291448	0.2051109	9.157785	-5.505046	0.0003552	0.0073112	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
Q9HCB6	-2.0954145	0.3709577	8.694096	-5.648661	0.0003565	0.0073112	Spondin-1
P12814	-1.9016090	0.3272561	8.209855	-5.810766	0.0003631	0.0073112	Alpha-actinin-1
P48163	-1.9351889	0.3194213	7.625022	-6.058422	0.0003665	0.0073112	NADP-dependent malic enzyme
Q9UQ35	-1.2247564	0.2262830	9.401099	-5.412499	0.0003666	0.0073112	Serine/arginine repetitive matrix protein 2
Q53GG5-2	-2.4399434	0.4284092	8.409844	-5.695357	0.0003804	0.0073955	PDZ and LIM domain protein 3
Q5M9N0	-2.7584485	0.4838290	8.385642	-5.701288	0.0003818	0.0073955	Coiled-coil domain-containing protein 158
P25940	-1.6429098	0.3016823	9.155619	-5.445828	0.0003843	0.0073955	Collagen alpha-3(V) chain
P07585	-2.1323372	0.3939309	9.259753	-5.412972	0.0003860	0.0073955	Decorin
Q9Y3B4	-1.2875533	0.2358882	9.068421	-5.458321	0.0003909	0.0073955	Splicing factor 3B subunit 6
P19429	2.2365865	0.3894775	8.211191	5.742531	0.0003929	0.0073955	Troponin I, cardiac muscle
P50453	-1.2078225	0.2212061	8.998589	-5.460168	0.0004006	0.0073955	Serpin B9
P49458	-1.8786710	0.3049990	7.251835	-6.159597	0.0004026	0.0073955	Signal recognition particle 9 kDa protein
Q53T59	-1.8080103	0.3124888	8.037638	-5.785841	0.0004046	0.0073955	HCLS1-binding protein 3
Q9UNW9	3.3060326	0.6115675	9.142176	5.405834	0.0004072	0.0073955	RNA-binding protein Nova-2
P02747	-1.8530999	0.2992016	7.043683	-6.193483	0.0004371	0.0078686	Complement C1q subcomponent subunit C
O94919	-1.1297756	0.2120168	9.184104	-5.328709	0.0004443	0.0078985	Endonuclease domain-containing 1 protein
P01008	-1.5453986	0.2930302	9.376569	-5.273855	0.0004466	0.0078985	Antithrombin-III
Q00G26	1.4810539	0.2531323	7.603807	5.850908	0.0004631	0.0081128	Perilipin-5
O00264	-1.4077482	0.2648534	9.097380	-5.315198	0.0004670	0.0081128	Membrane-associated progesterone receptor component 1
O60760	-2.2693850	0.4113993	8.420359	-5.516259	0.0004707	0.0081128	Hematopoietic prostaglandin D synthase
Q6SZW1	-2.0732831	0.3507879	7.420359	-5.910361	0.0004764	0.0081432	Sterile alpha and TIR motif-containing protein 1
Q9ULC3	-1.4313739	0.2673476	8.720682	-5.353981	0.0005115	0.0086695	Ras-related protein Rab-23
Q9BS26	-1.1794250	0.2286961	9.354832	-5.157170	0.0005282	0.0088132	Endoplasmic reticulum resident protein 44
Q9BTV4	-1.5944595	0.3074186	9.211817	-5.186607	0.0005329	0.0088132	Transmembrane protein 43
P14543	-1.3732462	0.2639990	9.153301	-5.201711	0.0005330	0.0088132	Nidogen-1
Q8WZA9	-1.0848657	0.2099434	9.231251	-5.167419	0.0005434	0.0088703	Immunity-related GTPase family Q protein
P08603	-1.1479994	0.2242815	9.420359	-5.118564	0.0005451	0.0088703	Complement factor H
Q9UKR5	-3.6937409	0.6993749	8.547992	-5.281489	0.0005997	0.0096809	Probable ergosterol biosynthetic protein 28
Q2TAA5	-1.1153927	0.2205888	9.234456	-5.056435	0.0006323	0.0100698	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
P11586	1.2736427	0.2359841	8.048875	5.397156	0.0006350	0.0100698	C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
P13671	-1.3576211	0.2715324	9.420359	-4.999850	0.0006439	0.0100698	Complement component C6
Q8WY22	-1.5074312	0.2863698	8.420359	-5.263932	0.0006441	0.0100698	BRI3-binding protein
Q9UJC5	-1.2143605	0.2426818	9.380287	-5.003921	0.0006485	0.0100698	SH3 domain-binding glutamic acid-rich-like protein 2
O14967	-1.6233066	0.3133456	8.580509	-5.180563	0.0006742	0.0103497	Calmegin
Q6PI78	1.5422623	0.3059022	9.092174	5.041684	0.0006767	0.0103497	Transmembrane protein 65
P01042	-1.9829048	0.3533886	7.306380	-5.611117	0.0006944	0.0105398	Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q8WWQ0	-1.3446280	0.2737312	9.420359	-4.912220	0.0007291	0.0109135	PH-interacting protein
P20774	-1.9551933	0.3711074	8.070059	-5.268538	0.0007355	0.0109135	Mimecan
Q9HAT2	1.5992357	0.3240018	9.271229	4.935885	0.0007390	0.0109135	Sialate O-acetylesterase
Q92621	-1.2226648	0.2494199	9.417394	-4.902035	0.0007404	0.0109135	Nuclear pore complex protein Nup205
Q12996	-1.6262833	0.2731239	6.493841	-5.954380	0.0007514	0.0109948	Cleavage stimulation factor subunit 3
Q8TDB4	-2.3381087	0.3865801	6.286039	-6.048187	0.0007778	0.0112937	Protein MGARP
Q16082	-1.2629563	0.2554732	9.059375	-4.943596	0.0007829	0.0112937	Heat shock protein beta-2
Q9BUH6	-1.0828646	0.2209139	9.196292	-4.901749	0.0007940	0.0113017	Protein PAXX
P02461	-2.9334098	0.5751845	8.416773	-5.099946	0.0007947	0.0113017	Collagen alpha-1(III) chain
Q14314	-1.9054905	0.3930629	9.417394	-4.847800	0.0008001	0.0113017	Fibroleukin
P45877	-0.9878277	0.2050408	9.420359	-4.817713	0.0008347	0.0116661	Peptidyl-prolyl cis-trans isomerase C
P35052	-1.2972987	0.2480341	7.847326	-5.230325	0.0008431	0.0116661	Glypican-1;Secreted glypican-1
P02790	-1.3146905	0.2731216	9.406717	-4.813571	0.0008431	0.0116661	Hemopexin
P01034	-1.4676678	0.2975753	8.859133	-4.932090	0.0008496	0.0116764	Cystatin-C
P50479	-2.0822296	0.4098960	8.192026	-5.079898	0.0008863	0.0120871	PDZ and LIM domain protein 4
P40261	-1.4439118	0.3008934	9.273912	-4.798749	0.0008965	0.0120871	Nicotinamide N-methyltransferase
Q86VP6	-1.3506010	0.2719850	8.552957	-4.965719	0.0009013	0.0120871	Cullin-associated NEDD8-dissociated protein 1
Q86VU5	1.3843626	0.2906522	9.420359	4.762952	0.0009033	0.0120871	Catechol O-methyltransferase domain-containing protein 1
P28300	-1.4644405	0.2835416	7.825199	-5.164816	0.0009203	0.0122349	Protein-lysine 6-oxidase
Q9HAV4	-1.8358132	0.3527066	7.670496	-5.204930	0.0009344	0.0123394	Exportin-5
O95183	-1.4512639	0.3064853	9.420359	-4.735183	0.0009403	0.0123394	Vesicle-associated membrane protein 5
P06727	-1.0726685	0.2210343	8.840955	-4.852951	0.0009521	0.0124060	Apolipoprotein A-IV
Q9NRX4	1.4050508	0.2956184	9.271509	4.752920	0.0009578	0.0124060	14 kDa phosphohistidine phosphatase
Q15126	-0.9960340	0.2111020	9.420359	-4.718261	0.0009637	0.0124060	Phosphomevalonate kinase
Q96H79	-2.2370397	0.3829114	6.200924	-5.842187	0.0009863	0.0126172	Zinc finger CCCH-type antiviral protein 1-like
O43175	-2.0597036	0.4346794	9.221484	-4.738443	0.0009925	0.0126175	D-3-phosphoglycerate dehydrogenase
Q15582	-2.2645249	0.4552646	8.068084	-4.974086	0.0010605	0.0133968	Transforming growth factor-beta-induced protein ig-h3
P13667	-1.0953363	0.2331484	9.172218	-4.698022	0.0010670	0.0133968	Protein disulfide-isomerase A4
O43143	-0.8789725	0.1894011	9.420359	-4.640801	0.0010789	0.0134630	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
Q09161	1.9700086	0.3456614	6.213723	5.699243	0.0011179	0.0138642	Nuclear cap-binding protein subunit 1
P34932	-0.8861862	0.1914748	9.291753	-4.628214	0.0011396	0.0140482	Heat shock 70 kDa protein 4
Q9UKX3	1.7720370	0.3833701	9.238422	4.622261	0.0011671	0.0143000	Myosin-13
Q9NY15	-1.4385610	0.3138718	9.403688	-4.583275	0.0011793	0.0143640	Stabilin-1
P46940	-1.1105871	0.2420668	9.239820	-4.587936	0.0012261	0.0148443	Ras GTPase-activating-like protein IQGAP1
P26447	-1.4990741	0.3207602	8.758554	-4.673504	0.0012510	0.0150561	Protein S100-A4
O60262	-1.2559109	0.2689796	8.700017	-4.669167	0.0012814	0.0153110	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
O95445	-2.5298428	0.5522077	9.101762	-4.581324	0.0012872	0.0153110	Apolipoprotein M
Q96CS3	-1.1510089	0.2514113	9.091487	-4.578191	0.0012968	0.0153355	FAS-associated factor 2
P00747	-0.8238672	0.1828138	9.406119	-4.506593	0.0013198	0.0154483	Plasminogen;Plasmin heavy chain A;Activation peptide;Angiostatin;Plasmin heavy chain A, short form;Plasmin light chain B
Q96JB2	-2.0512914	0.4358269	8.420359	-4.706665	0.0013299	0.0154483	Conserved oligomeric Golgi complex subunit 3
Q6UWS5	1.3529266	0.2687275	7.292033	5.034567	0.0013327	0.0154483	Protein PET117 homolog, mitochondrial
P27658	-1.6133702	0.3588925	9.420359	-4.495414	0.0013367	0.0154483	Collagen alpha-1(VIII) chain;Vastatin
P01019	-1.0239723	0.2255684	9.127320	-4.539521	0.0013573	0.0155978	Angiotensinogen;Angiotensin-1;Angiotensin-2;Angiotensin-3;Angiotensin-4;Angiotensin 1-9;Angiotensin 1-7;Angiotensin 1-5;Angiotensin 1-4
Q9BXV9	1.4430515	0.3205010	9.289309	4.502487	0.0013702	0.0156569	Uncharacterized protein C14orf142
Q07507	-1.2545210	0.2616825	7.928623	-4.794058	0.0014005	0.0159141	Dermatopontin
P09619	-1.2391198	0.2758540	9.226613	-4.491941	0.0014154	0.0159936	Platelet-derived growth factor receptor beta
P02748	-1.2229145	0.2693768	8.912977	-4.539792	0.0014417	0.0162007	Complement component C9;Complement component C9a;Complement component C9b
Q96LL9	-1.2440322	0.2745771	8.810329	-4.530722	0.0015041	0.0168091	DnaJ homolog subfamily C member 30
Q92930	-1.4774889	0.3083082	7.661957	-4.792246	0.0015442	0.0171433	Ras-related protein Rab-8B
Q04721	1.1483233	0.2590956	9.213519	4.432045	0.0015508	0.0171433	Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
Q99983	-2.9528995	0.5885590	6.949931	-5.017168	0.0015683	0.0171916	Osteomodulin
Q9UQR1	-1.7724910	0.3607923	7.233799	-4.912773	0.0015721	0.0171916	Zinc finger protein 148
P03950	-1.7791248	0.3848924	8.205145	-4.622395	0.0015950	0.0173485	Angiogenin
O95486	-1.3819063	0.3118915	9.078202	-4.430728	0.0016110	0.0174297	Protein transport protein Sec24A
P54577	-1.0184999	0.2299667	9.016679	-4.428901	0.0016423	0.0176342	Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
P83916	-1.6056296	0.3090985	6.420359	-5.194557	0.0016473	0.0176342	Chromobox protein homolog 1
Q9UBV8	-1.1380629	0.2569081	8.957298	-4.429844	0.0016668	0.0177499	Peflin
Q7Z3T8	-1.3746348	0.3062168	8.586144	-4.489090	0.0017016	0.0180268	Zinc finger FYVE domain-containing protein 16
P00352	-1.1346512	0.2499228	8.251350	-4.540007	0.0017550	0.0181316	Retinal dehydrogenase 1
P62857	-1.3551185	0.2898757	7.713404	-4.674826	0.0017560	0.0181316	40S ribosomal protein S28
P15924	0.9266546	0.2145531	9.383746	4.318998	0.0017566	0.0181316	Desmoplakin
P80723	-1.5107829	0.3290664	8.027411	-4.591119	0.0017602	0.0181316	Brain acid soluble protein 1
O15061	-1.1041834	0.2561457	9.420359	-4.310763	0.0017625	0.0181316	Synemin
Q9H1E5	-1.0067111	0.2335851	9.420359	-4.309826	0.0017650	0.0181316	Thioredoxin-related transmembrane protein 4
O75489	1.0163873	0.2360292	9.420359	4.306192	0.0017747	0.0181398	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
P19447	-1.5879548	0.3346186	7.420359	-4.745567	0.0017864	0.0181672	TFIIH basal transcription factor complex helicase XPB subunit
Q9NS69	-1.0847694	0.2462880	8.795400	-4.404475	0.0018070	0.0182856	Mitochondrial import receptor subunit TOM22 homolog
Q96CX2	-0.9045513	0.2112848	9.341232	-4.281195	0.0018791	0.0188636	BTB/POZ domain-containing protein KCTD12
Q08945	-1.3761500	0.3092502	8.420359	-4.449956	0.0018856	0.0188636	FACT complex subunit SSRP1
Q9NS86	-0.9960486	0.2309453	9.124467	-4.312920	0.0018919	0.0188636	LanC-like protein 2
O15118	-2.1247916	0.4204381	6.420359	-5.053756	0.0019057	0.0189078	Niemann-Pick C1 protein
Q9Y287	-1.6105936	0.3777397	9.358076	-4.263766	0.0019212	0.0189117	Integral membrane protein 2B;BRI2, membrane form;BRI2 intracellular domain;BRI2C, soluble form;Bri23 peptide
Q9BYN0	-1.2801043	0.2981602	9.171396	-4.293345	0.0019246	0.0189117	Sulfiredoxin-1
P52907	-0.8523732	0.2010137	9.420359	-4.240373	0.0019610	0.0190197	F-actin-capping protein subunit alpha-1
Q9UBB5	1.4388020	0.2863146	6.420359	5.025248	0.0019633	0.0190197	Methyl-CpG-binding domain protein 2
P62328	-1.3455146	0.2900067	7.519371	-4.639599	0.0019637	0.0190197	Thymosin beta-4;Hematopoietic system regulatory peptide
Q8N142	1.0768090	0.2532957	9.279649	4.251193	0.0019957	0.0192379	Adenylosuccinate synthetase isozyme 1
P82663	-1.3399129	0.3170820	9.372918	-4.225761	0.0020278	0.0194551	28S ribosomal protein S25, mitochondrial
Q14118	-0.8487363	0.1972071	8.781740	-4.303782	0.0020956	0.0200113	Dystroglycan;Alpha-dystroglycan;Beta-dystroglycan
P50991	-1.5101244	0.3463126	8.464244	-4.360581	0.0021080	0.0200355	T-complex protein 1 subunit delta
P31323	-0.9232942	0.2193346	9.248862	-4.209524	0.0021407	0.0202522	cAMP-dependent protein kinase type II-beta regulatory subunit
Q8NAT1	-0.8308927	0.1986691	9.360836	-4.182296	0.0021724	0.0204572	Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Q07065	-0.9488623	0.2235778	8.959731	-4.243992	0.0021835	0.0204668	Cytoskeleton-associated protein 4
P61009	-0.8882212	0.2066525	8.595403	-4.298139	0.0022203	0.0207006	Signal peptidase complex subunit 3
A5D6W6	-2.1994339	0.4937525	7.849139	-4.454527	0.0022288	0.0207006	Fat storage-inducing transmembrane protein 1
P07384	-0.8641607	0.2077173	9.301416	-4.160273	0.0022778	0.0210594	Calpain-1 catalytic subunit
Q6IC98	-0.9057366	0.2125145	8.655845	-4.262000	0.0023004	0.0211723	GRAM domain-containing protein 4
Q96AG4	-1.0641384	0.2572887	9.349851	-4.135970	0.0023374	0.0214156	Leucine-rich repeat-containing protein 59
P05455	-0.8562036	0.2063184	9.171164	-4.149914	0.0023855	0.0217457	Lupus La protein
Q12988	-1.0103210	0.2443755	9.255593	-4.134297	0.0023948	0.0217457	Heat shock protein beta-3
Q04760	1.3958984	0.3318358	8.783089	4.206593	0.0024115	0.0218004	Lactoylglutathione lyase
P50238	-1.7621993	0.4214564	8.861059	-4.181214	0.0024543	0.0220228	Cysteine-rich protein 1
P62277	-1.3005300	0.3173121	9.380882	-4.098583	0.0024578	0.0220228	40S ribosomal protein S13
P61925	1.3913131	0.3131368	7.546436	4.443148	0.0024919	0.0222302	cAMP-dependent protein kinase inhibitor alpha
Q9H1K0	-1.6022771	0.3584229	7.420359	-4.470353	0.0025098	0.0222484	Rabenosyn-5
Q8IYI6	-0.9330152	0.2287206	9.409497	-4.079280	0.0025158	0.0222484	Exocyst complex component 8
P13796	-0.8819572	0.2143660	9.129666	-4.114258	0.0025417	0.0223806	Plastin-2
P05543	-1.1801143	0.2649281	7.348700	-4.454470	0.0026223	0.0229058	Thyroxine-binding globulin
Q9UK22	-1.3974278	0.2938770	6.412167	-4.755145	0.0026280	0.0229058	F-box only protein 2
Q96A65	-0.8321129	0.2055547	9.417394	-4.048133	0.0026352	0.0229058	Exocyst complex component 4
P62745	-1.1929691	0.2879947	8.729889	-4.142330	0.0026838	0.0231598	Rho-related GTP-binding protein RhoB
P58546	-1.2963604	0.3163198	8.948856	-4.098259	0.0027162	0.0231598	Myotrophin
P24311	1.1056319	0.2745010	9.420359	4.027789	0.0027178	0.0231598	Cytochrome c oxidase subunit 7B, mitochondrial
Q96FN9	-1.7766077	0.4243295	8.420359	-4.186859	0.0027240	0.0231598	Probable D-tyrosyl-tRNA(Tyr) deacylase 2
O00625	-1.1028338	0.2740332	9.420359	-4.024453	0.0027318	0.0231598	Pirin
Q9Y490	-0.8597753	0.2118978	9.188565	-4.057500	0.0027327	0.0231598	Talin-1
O75348	-1.2891767	0.3206941	9.420359	-4.019958	0.0027510	0.0232176	V-type proton ATPase subunit G 1
P04843	-1.5241453	0.3692851	8.671925	-4.127286	0.0027829	0.0233905	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
Q9UL18	-1.3184619	0.3107203	7.913528	-4.243243	0.0028955	0.0240366	Protein argonaute-1
Q8N5M1	-1.2833584	0.3185222	9.122947	-4.029103	0.0028956	0.0240366	ATP synthase mitochondrial F1 complex assembly factor 2
Q6P1N0	-1.6508051	0.3697603	6.982437	-4.464527	0.0029383	0.0240366	Coiled-coil and C2 domain-containing protein 1A
Q96GK7	-1.2557512	0.2967899	7.910446	-4.231112	0.0029459	0.0240366	Fumarylacetoacetate hydrolase domain-containing protein 2A
Q9NQZ5	1.3550021	0.3376320	9.152040	4.013252	0.0029470	0.0240366	StAR-related lipid transfer protein 7, mitochondrial
Q9NNX1	3.4412993	0.7408907	6.420359	4.644813	0.0029547	0.0240366	Tuftelin
P63316	0.8794535	0.2214963	9.420359	3.970512	0.0029707	0.0240366	Troponin C, slow skeletal and cardiac muscles
Q15125	-1.5522594	0.3856163	9.031289	-4.025399	0.0029725	0.0240366	3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Q9Y4W6	0.9189304	0.2304862	9.296575	3.986921	0.0029732	0.0240366	AFG3-like protein 2
Q9HB40	-1.4736038	0.3162446	6.361260	-4.659697	0.0029780	0.0240366	Retinoid-inducible serine carboxypeptidase
Q3ZCW2	-1.3933792	0.3111768	6.883416	-4.477773	0.0029961	0.0240872	Galectin-related protein
Q96C86	-0.8529077	0.2132782	9.149198	-3.999038	0.0030135	0.0241315	m7GpppX diphosphatase
Q9UKS6	0.9882506	0.2462779	8.991910	4.012745	0.0030568	0.0243623	Protein kinase C and casein kinase substrate in neurons protein 3
P00492	-0.9642312	0.2405131	9.002876	-4.009058	0.0030662	0.0243623	Hypoxanthine-guanine phosphoribosyltransferase
Q00577	-1.0249972	0.2562123	8.997651	-4.000578	0.0031094	0.0246086	Transcriptional activator protein Pur-alpha
P14555	-3.1616763	0.7143843	6.916563	-4.425736	0.0031505	0.0248378	Phospholipase A2, membrane associated
Q53FA7	1.3758827	0.3477833	9.200370	3.956150	0.0031824	0.0249922	Quinone oxidoreductase PIG3
P09467	-1.4304382	0.3334940	7.273827	-4.289247	0.0033074	0.0258738	Fructose-1,6-bisphosphatase 1
P25311	-1.0782056	0.2680130	8.556242	-4.022960	0.0033319	0.0259657	Zinc-alpha-2-glycoprotein
Q9UHD9	-0.8978150	0.2281566	9.081182	-3.935083	0.0033718	0.0261766	Ubiquilin-2
P01303	-1.3886725	0.3523281	8.990424	-3.941419	0.0034057	0.0262520	Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
P50552	-0.9233883	0.2346915	9.036834	-3.934477	0.0034073	0.0262520	Vasodilator-stimulated phosphoprotein
Q7L4E1	-1.9056994	0.4888519	9.203928	-3.898317	0.0034763	0.0266529	Protein FAM73B
O95810	-0.7267426	0.1876918	9.391488	-3.871999	0.0034856	0.0266529	Serum deprivation-response protein
P53618	-0.9076351	0.2349409	9.420359	-3.863249	0.0035135	0.0267061	Coatomer subunit beta
Q8IYU8	-3.0629900	0.6825201	6.420359	-4.487766	0.0035188	0.0267061	Calcium uptake protein 2, mitochondrial
Q9BVC6	-1.1958920	0.3101095	9.420359	-3.856354	0.0035518	0.0268562	Transmembrane protein 109
Q96MM6	1.8061841	0.4138998	6.744197	4.363819	0.0036037	0.0271480	Heat shock 70 kDa protein 12B
O15031	-0.9094327	0.2339821	9.058686	-3.886762	0.0036477	0.0273776	Plexin-B2
Q92575	-0.9922287	0.2530061	8.755899	-3.921758	0.0036939	0.0276226	UBX domain-containing protein 4
Q8IUX7	-2.3978246	0.5007151	5.557874	-4.788800	0.0037286	0.0277802	Adipocyte enhancer-binding protein 1
P28070	-0.9263111	0.2288931	7.931934	-4.046916	0.0037665	0.0278924	Proteasome subunit beta type-4
Q7KZF4	-0.8794696	0.2306324	9.420359	-3.813296	0.0038010	0.0278924	Staphylococcal nuclease domain-containing protein 1
P21980	-0.9178411	0.2371165	8.976904	-3.870844	0.0038023	0.0278924	Protein-glutamine gamma-glutamyltransferase 2
Q14258	-0.9919848	0.2493945	8.251367	-3.977573	0.0038293	0.0278924	E3 ubiquitin/ISG15 ligase TRIM25
A6NDG6	1.0711621	0.2790153	9.171051	3.839080	0.0038355	0.0278924	Phosphoglycolate phosphatase
Q9Y2D4	-1.5165389	0.3887140	8.722544	-3.901426	0.0038359	0.0278924	Exocyst complex component 6B
P27695	-1.4919668	0.3919125	9.420359	-3.806887	0.0038397	0.0278924	DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial
P43121	-1.0780079	0.2743745	8.511897	-3.928965	0.0038622	0.0279563	Cell surface glycoprotein MUC18
P14625	-0.9671286	0.2543051	9.403167	-3.803025	0.0038760	0.0279565	Endoplasmin
Q9Y5U8	-2.4800568	0.6509890	9.319580	-3.809676	0.0038984	0.0280191	Mitochondrial pyruvate carrier 1
P10109	0.8708452	0.2279286	9.175781	3.820693	0.0039427	0.0282373	Adrenodoxin, mitochondrial
E5RK69	-1.1254137	0.2972634	9.420359	-3.785914	0.0039690	0.0283264	Annexin
Q15738	-1.0818010	0.2866379	9.420359	-3.774103	0.0040439	0.0285565	Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
P62312	-1.5682756	0.4061040	8.734633	-3.861759	0.0040596	0.0285565	U6 snRNA-associated Sm-like protein LSm6
Q01581	-1.5736067	0.3821137	7.316536	-4.118163	0.0040634	0.0285565	Hydroxymethylglutaryl-CoA synthase, cytoplasmic
Q9BWJ5	-1.1786521	0.3126119	9.420359	-3.770336	0.0040681	0.0285565	Splicing factor 3B subunit 5
Q96PK6	-0.9252023	0.2430058	9.118686	-3.807326	0.0040715	0.0285565	RNA-binding protein 14
P04207	-1.4064185	0.3683423	8.973244	-3.818238	0.0041235	0.0288222	Ig kappa chain V-III region CLL
Q13636	-1.9750968	0.4490568	6.233646	-4.398323	0.0041780	0.0290215	Ras-related protein Rab-31
P78406	-1.6990379	0.3883613	6.300617	-4.374890	0.0041812	0.0290215	mRNA export factor
P31949	-0.9710473	0.2584858	9.372327	-3.756676	0.0041948	0.0290215	Protein S100-A11;Protein S100-A11, N-terminally processed
P27169	-1.0408608	0.2734080	8.938402	-3.806987	0.0042252	0.0290356	Serum paraoxonase/arylesterase 1
P49773	-0.9406572	0.2511758	9.420359	-3.745015	0.0042347	0.0290356	Histidine triad nucleotide-binding protein 1
Q96EM0	-1.2281296	0.3150239	8.300560	-3.898529	0.0042397	0.0290356	Trans-3-hydroxy-L-proline dehydratase
Q9BT09	-1.2017444	0.3180938	9.105218	-3.777957	0.0042723	0.0291493	Protein canopy homolog 3
P01699	-1.9617461	0.4506972	6.301890	-4.352692	0.0042850	0.0291493	Ig lambda chain V-I region VOR
Q2TAY7	-1.0380001	0.2752559	9.116096	-3.771036	0.0043092	0.0292163	WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed
Q04941	-1.3354806	0.3557294	9.122186	-3.754203	0.0044181	0.0297125	Proteolipid protein 2
P00488	-1.1450813	0.3065552	9.274740	-3.735319	0.0044192	0.0297125	Coagulation factor XIII A chain
P01611	-1.3210912	0.3554033	9.420359	-3.717161	0.0044262	0.0297125	Ig kappa chain V-I region Wes
Q9UNN8	-1.2379487	0.3244063	8.506448	-3.816044	0.0045663	0.0305523	Endothelial protein C receptor
P07360	-0.9508577	0.2519801	8.758820	-3.773543	0.0046128	0.0307619	Complement component C8 gamma chain
Q9BXF6	-0.8964783	0.2431075	9.420359	-3.687580	0.0046396	0.0308071	Rab11 family-interacting protein 5
Q5JUQ0	2.8054144	0.6808551	6.864054	4.120428	0.0046498	0.0308071	Protein FAM78A
Q02818	-1.1067621	0.2711064	6.995049	-4.082390	0.0046826	0.0308706	Nucleobindin-1
Q9HBL0	1.0363941	0.2720098	8.420359	3.810135	0.0046939	0.0308706	Tensin-1
Q96KP1	-1.0392328	0.2587608	7.267948	-4.016191	0.0047050	0.0308706	Exocyst complex component 2
O75165	-0.7578962	0.2049879	9.231691	-3.697272	0.0047298	0.0309079	DnaJ homolog subfamily C member 13
P20042	-0.8792944	0.2376566	9.197242	-3.699852	0.0047410	0.0309079	Eukaryotic translation initiation factor 2 subunit 2
P46063	-0.7705141	0.2085324	9.183164	-3.694937	0.0047903	0.0309698	ATP-dependent DNA helicase Q1
Q8IVD9	-0.9380220	0.2450845	8.198729	-3.827341	0.0048105	0.0309698	NudC domain-containing protein 3
P10643	-1.1503065	0.3113889	9.159735	-3.694115	0.0048176	0.0309698	Complement component C7
P31689	-1.4848105	0.3875317	8.155261	-3.831456	0.0048300	0.0309698	DnaJ homolog subfamily A member 1
Q13011	0.8580498	0.2299097	8.838577	3.732116	0.0048338	0.0309698	Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Q04837	-1.2706968	0.3386600	8.651174	-3.752131	0.0048713	0.0309698	Single-stranded DNA-binding protein, mitochondrial
Q9BU61	-1.2937160	0.3537628	9.420359	-3.657015	0.0048714	0.0309698	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3
Q9BXR6	-1.3408193	0.3666219	9.417394	-3.657227	0.0048723	0.0309698	Complement factor H-related protein 5
Q08357	-1.2512681	0.3317594	8.465455	-3.771613	0.0049202	0.0311310	Sodium-dependent phosphate transporter 2
Q53GG5	1.0396066	0.2802467	8.915226	3.709613	0.0049283	0.0311310	PDZ and LIM domain protein 3
Q9Y5U9	-0.9688010	0.2537423	8.113937	-3.818051	0.0049709	0.0313029	Immediate early response 3-interacting protein 1
Q8NDY3	1.2548368	0.3412954	9.066122	3.676689	0.0050383	0.0316295	[Protein ADP-ribosylarginine] hydrolase-like protein 1
Q9HCN8	-0.8376149	0.2299564	9.325084	-3.642495	0.0050707	0.0317347	Stromal cell-derived factor 2-like protein 1
Q9UBI9	-1.9350473	0.4883540	7.231219	-3.962387	0.0050999	0.0318195	Headcase protein homolog
O75663	-1.6975991	0.4618211	8.989551	-3.675880	0.0051181	0.0318358	TIP41-like protein
P00918	-0.9493414	0.2613767	9.327391	-3.632081	0.0051532	0.0318941	Carbonic anhydrase 2
Q8TDB6	-0.9819803	0.2685382	9.102046	-3.656762	0.0051629	0.0318941	E3 ubiquitin-protein ligase DTX3L
Q9Y5J7	-1.4394711	0.3977241	9.420359	-3.619271	0.0051746	0.0318941	Mitochondrial import inner membrane translocase subunit Tim9
P61020	-0.8349426	0.2271616	8.866958	-3.675545	0.0052423	0.0321784	Ras-related protein Rab-5B
O15121	-1.3734454	0.3782388	9.228763	-3.631159	0.0052523	0.0321784	Sphingolipid delta(4)-desaturase DES1
O00299	-0.9153236	0.2528154	9.304824	-3.620521	0.0052698	0.0321887	Chloride intracellular channel protein 1
Q8NBF2	-0.8115466	0.2248622	9.347444	-3.609084	0.0053267	0.0323921	NHL repeat-containing protein 2
P31994-2	-0.7713913	0.2123017	9.122267	-3.633466	0.0053350	0.0323921	Low affinity immunoglobulin gamma Fc region receptor II-b
Q8WUM0	-0.7928646	0.2201827	9.277093	-3.600940	0.0054630	0.0330708	Nuclear pore complex protein Nup133
Q15493	-1.5865116	0.4375846	9.005754	-3.625611	0.0055174	0.0333009	Regucalcin
P46777	-1.0578875	0.2897786	8.757208	-3.650676	0.0055626	0.0334533	60S ribosomal protein L5
P00742	-1.3361965	0.3268762	6.419136	-4.087775	0.0055841	0.0334533	Coagulation factor X;Factor X light chain;Factor X heavy chain;Activated factor Xa heavy chain
O00567	-1.6066654	0.4489340	9.345669	-3.578845	0.0055920	0.0334533	Nucleolar protein 56
P49756	-0.8733625	0.2452468	9.420359	-3.561158	0.0056804	0.0338825	RNA-binding protein 25
Q9H4A6	-0.9863755	0.2771451	9.333154	-3.559058	0.0057841	0.0344004	Golgi phosphoprotein 3
Q6PCE3	-1.3068366	0.3405543	7.360778	-3.837380	0.0058132	0.0344727	Glucose 1,6-bisphosphate synthase
O15144	-1.0266458	0.2845878	8.851301	-3.607483	0.0058393	0.0345266	Actin-related protein 2/3 complex subunit 2
Q6P1L8	0.6856534	0.1923234	9.202756	3.565107	0.0058582	0.0345381	39S ribosomal protein L14, mitochondrial
P24752	0.8145171	0.2270837	8.915799	3.586858	0.0059577	0.0350232	Acetyl-CoA acetyltransferase, mitochondrial
P06396	-1.1557324	0.3175614	8.455087	-3.639398	0.0060041	0.0351939	Gelsolin
Q1KMD3	-0.9588418	0.2691474	9.065422	-3.562515	0.0060251	0.0352156	Heterogeneous nuclear ribonucleoprotein U-like protein 2
Q96PE7	-1.1472298	0.3258058	9.420359	-3.521208	0.0060579	0.0353060	Methylmalonyl-CoA epimerase, mitochondrial
Q9HAN9	1.2305740	0.3230453	7.321157	3.809293	0.0060984	0.0354402	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
P56199	-0.8817502	0.2451200	8.643688	-3.597218	0.0061682	0.0356539	Integrin alpha-1
Q9Y646	-0.6906706	0.1960589	9.294244	-3.522770	0.0061702	0.0356539	Carboxypeptidase Q
P62330	-0.7931556	0.2242913	9.122775	-3.536275	0.0062172	0.0358132	ADP-ribosylation factor 6
Q9UBS4	-1.7470606	0.4930682	9.044784	-3.543244	0.0062330	0.0358132	DnaJ homolog subfamily B member 11
P17050	-0.9454418	0.2682555	9.156208	-3.524408	0.0062990	0.0360905	Alpha-N-acetylgalactosaminidase
Q9Y5Z7	-1.9019574	0.4680155	6.116460	-4.063877	0.0063592	0.0362794	Host cell factor 2
P01597	-2.2333895	0.6327136	9.042973	-3.529859	0.0063676	0.0362794	Ig kappa chain V-I region DEE
P05062	-2.0647894	0.5508210	7.417394	-3.748567	0.0064626	0.0367177	Fructose-bisphosphate aldolase B
P62191	-1.0000517	0.2855948	9.201844	-3.501645	0.0064811	0.0367200	26S protease regulatory subunit 4
Q8TCJ2	-0.8698436	0.2465217	8.921075	-3.528467	0.0065189	0.0368316	Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit STT3B
Q9H9B4	-0.7776690	0.2196810	8.758716	-3.539992	0.0065917	0.0371397	Sideroflexin-1
P08754	-1.0292580	0.2979223	9.420359	-3.454787	0.0067445	0.0375627	Guanine nucleotide-binding protein G(k) subunit alpha
P30050	-1.1309945	0.3257840	9.240612	-3.471608	0.0067562	0.0375627	60S ribosomal protein L12
Q68DH5	-0.9839434	0.2752828	8.344587	-3.574301	0.0067644	0.0375627	LMBR1 domain-containing protein 2
Q14019	-2.3417241	0.5964209	6.420359	-3.926294	0.0067706	0.0375627	Coactosin-like protein
P23284	-0.7744408	0.2214611	8.982458	-3.496960	0.0067761	0.0375627	Peptidyl-prolyl cis-trans isomerase B
P60903	-0.8289441	0.2386403	9.201691	-3.473613	0.0067775	0.0375627	Protein S100-A10
O43920	0.8295850	0.2386795	9.164468	3.475728	0.0067962	0.0375640	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
Q9GZY4	-1.6172207	0.4432059	7.775949	-3.648916	0.0068292	0.0376440	Cytochrome c oxidase assembly factor 1 homolog
P15848	0.9204565	0.2603319	8.570614	3.535704	0.0068679	0.0376645	Arylsulfatase B
Q9HAV7	0.8532336	0.2459635	9.164544	3.468945	0.0068700	0.0376645	GrpE protein homolog 1, mitochondrial
O14807	-0.9860449	0.2846002	9.178081	-3.464667	0.0069016	0.0377246	Ras-related protein M-Ras
Q9Y623	-1.9955095	0.5618523	8.399371	-3.551662	0.0069240	0.0377246	Myosin-4
P27797	-0.8755252	0.2546797	9.417394	-3.437751	0.0069366	0.0377246	Calreticulin
O75643	-0.7286175	0.2121708	9.420359	-3.434109	0.0069744	0.0378294	U5 small nuclear ribonucleoprotein 200 kDa helicase
Q12907	-1.6602075	0.4671559	8.313980	-3.553862	0.0070158	0.0378649	Vesicular integral-membrane protein VIP36
O75190-3	1.2231318	0.3565719	9.420359	3.430253	0.0070182	0.0378649	DnaJ homolog subfamily B member 6
P17540	0.9216483	0.2487257	7.298674	3.705481	0.0070540	0.0379570	Creatine kinase S-type, mitochondrial
O43290	-0.7436611	0.2171716	9.420359	-3.424301	0.0070863	0.0380306	U4/U6.U5 tri-snRNP-associated protein 1
P98160	-0.6944147	0.2022592	9.245897	-3.433291	0.0071780	0.0383683	Basement membrane-specific heparan sulfate proteoglycan core protein;Endorepellin;LG3 peptide
Q16204	-0.7607082	0.2190201	8.855932	-3.473235	0.0071870	0.0383683	Coiled-coil domain-containing protein 6
P21281	-1.3428216	0.3928941	9.377634	-3.417769	0.0072093	0.0383866	V-type proton ATPase subunit B, brain isoform
P30101	-0.7361350	0.2161032	9.401877	-3.406405	0.0073160	0.0388531	Protein disulfide-isomerase A3
Q6ZVF9	-1.5316163	0.3710478	5.510860	-4.127814	0.0073979	0.0391859	G protein-regulated inducer of neurite outgrowth 3
P41208	-1.1048997	0.3226308	9.121806	-3.424657	0.0074238	0.0392206	Centrin-2
O75533	-0.7480960	0.2199021	9.281221	-3.401950	0.0075073	0.0395594	Splicing factor 3B subunit 1
O43707	-1.3709413	0.3951980	8.554624	-3.468999	0.0076265	0.0400835	Alpha-actinin-4
P56192	-1.0251690	0.2985340	8.830575	-3.434010	0.0076742	0.0401467	Methionine–tRNA ligase, cytoplasmic
P32119	-0.8759792	0.2468160	7.897094	-3.549119	0.0076787	0.0401467	Peroxiredoxin-2
P55735	-0.9148870	0.2659790	8.745427	-3.439697	0.0077172	0.0401467	Protein SEC13 homolog
Q92805	1.3677629	0.3990676	8.858631	3.427396	0.0077177	0.0401467	Golgin subfamily A member 1
Q8NBJ5	-1.0090957	0.2932132	8.713942	-3.441508	0.0077372	0.0401467	Procollagen galactosyltransferase 1
P02749	-0.9821379	0.2881999	8.996525	-3.407836	0.0077806	0.0402690	Beta-2-glycoprotein 1
Q9UK41	-1.5562781	0.4606623	9.268585	-3.378349	0.0078138	0.0403382	Vacuolar protein sorting-associated protein 28 homolog
Q5VUM1	0.7587056	0.2245024	9.213910	3.379499	0.0078652	0.0405009	Succinate dehydrogenase assembly factor 4, mitochondrial
Q96G03	-0.8738839	0.2603156	9.420359	-3.357017	0.0079060	0.0406079	Phosphoglucomutase-2
P43686	-1.2985795	0.3875167	9.398102	-3.351029	0.0080098	0.0409929	26S protease regulatory subunit 6B
Q6ICB0	-2.0382992	0.5471065	6.695413	-3.725599	0.0080212	0.0409929	Desumoylating isopeptidase 1
P11021	-0.6930674	0.2048069	9.016794	-3.384004	0.0080539	0.0410209	78 kDa glucose-regulated protein
Q9BVG4	-1.4282890	0.4270292	9.419676	-3.344711	0.0080670	0.0410209	Protein PBDC1
Q6Y288	-1.0690665	0.3184078	9.258387	-3.357539	0.0080932	0.0410515	Beta-1,3-glucosyltransferase
Q9UBQ0	-1.1043560	0.3293908	9.239664	-3.352722	0.0081795	0.0413860	Vacuolar protein sorting-associated protein 29
P61026	-0.8659400	0.2443342	7.602181	-3.544081	0.0082280	0.0415280	Ras-related protein Rab-10
O60568	-1.0635431	0.3203369	9.420359	-3.320077	0.0083972	0.0422680	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Q14011	-1.6060873	0.4676141	8.287145	-3.434642	0.0084318	0.0422680	Cold-inducible RNA-binding protein
Q5T447	-1.0258262	0.3044486	8.870208	-3.369456	0.0084370	0.0422680	E3 ubiquitin-protein ligase HECTD3
P17174	0.8269867	0.2485633	9.191878	3.327066	0.0085865	0.0428091	Aspartate aminotransferase, cytoplasmic
Q96LD4	-2.0603233	0.5325761	5.888034	-3.868599	0.0085871	0.0428091	Tripartite motif-containing protein 47
Q9BX97	-1.3847012	0.3974417	7.758076	-3.484036	0.0086779	0.0431559	Plasmalemma vesicle-associated protein
P51692	-1.6950637	0.5096371	9.100029	-3.326021	0.0087208	0.0432637	Signal transducer and activator of transcription 5B
Q9HCJ6	-0.8677868	0.2633701	9.417394	-3.294932	0.0087533	0.0433192	Synaptic vesicle membrane protein VAT-1 homolog-like
Q9BSH5	-0.8065712	0.2419806	8.978305	-3.333206	0.0087837	0.0433643	Haloacid dehalogenase-like hydrolase domain-containing protein 3
P29992	-1.0018710	0.2959582	8.436243	-3.385178	0.0088516	0.0435938	Guanine nucleotide-binding protein subunit alpha-11
A4D2B0	-1.7140517	0.5055811	8.367083	-3.390261	0.0088896	0.0436751	Metallo-beta-lactamase domain-containing protein 1
P16455	-0.7988054	0.2358633	8.351627	-3.386731	0.0089616	0.0439229	Methylated-DNA–protein-cysteine methyltransferase
P05387	-0.7447264	0.2265778	9.261556	-3.286846	0.0090698	0.0443459	60S acidic ribosomal protein P2
P16083	-1.0028849	0.2977294	8.408267	-3.368444	0.0091246	0.0444935	Ribosyldihydronicotinamide dehydrogenase [quinone]
I3L505	1.1922390	0.3578892	8.742159	3.331308	0.0091437	0.0444935	Acyl carrier protein
O60927	-0.9472893	0.2671994	7.072548	-3.545252	0.0092452	0.0448802	Protein phosphatase 1 regulatory subunit 11
Q13425	-0.7615654	0.2331007	9.307500	-3.267109	0.0093039	0.0450325	Beta-2-syntrophin
Q8N392	2.3552996	0.6366348	6.272040	3.699609	0.0093209	0.0450325	Rho GTPase-activating protein 18
Q96CN7	-1.0144660	0.3102486	9.191660	-3.269849	0.0094174	0.0453910	Isochorismatase domain-containing protein 1
P01621	-1.1890923	0.3622603	8.991047	-3.282425	0.0095052	0.0457056	Ig kappa chain V-III region NG9
Q9UMR3	-1.6328959	0.4714071	7.420359	-3.463876	0.0095749	0.0459325	T-box transcription factor TBX20
Q9NX08	-0.7274661	0.2225081	8.998441	-3.269391	0.0096944	0.0463004	COMM domain-containing protein 8
O43592	-0.8026366	0.2477266	9.327348	-3.240009	0.0096971	0.0463004	Exportin-T
Q13825	1.3948092	0.4330846	9.420359	3.220639	0.0098829	0.0470010	Methylglutaconyl-CoA hydratase, mitochondrial
O95159	-1.7663091	0.5267649	8.061146	-3.353126	0.0099239	0.0470010	Zinc finger protein-like 1
O60503	1.2572380	0.3432644	6.207277	3.662594	0.0099335	0.0470010	Adenylate cyclase type 9
P35754	0.8371729	0.2590987	9.256564	3.231097	0.0099363	0.0470010	Glutaredoxin-1
Q6UXG3	1.6474617	0.5114802	9.266008	3.220969	0.0100882	0.0476088	CMRF35-like molecule 9
Q6B0K9	-1.3448839	0.3998344	7.854249	-3.363603	0.0101471	0.0477759	Hemoglobin subunit mu
P03915	-1.1507202	0.3495468	8.417376	-3.292035	0.0102419	0.0480857	NADH-ubiquinone oxidoreductase chain 5
P34947	-1.4080509	0.4396529	9.361568	-3.202642	0.0102602	0.0480857	G protein-coupled receptor kinase 5
Q13541	0.9175109	0.2871743	9.420359	3.194961	0.0103090	0.0482035	Eukaryotic translation initiation factor 4E-binding protein 1
O14656	-1.8183830	0.5541802	8.420359	-3.281212	0.0104087	0.0485580	Torsin-1A
P05060	-2.3136323	0.6771858	7.313959	-3.416540	0.0104618	0.0486940	Secretogranin-1;PE-11;GAWK peptide;CCB peptide
P14174	-0.8418646	0.2617826	9.024325	-3.215892	0.0105221	0.0488630	Macrophage migration inhibitory factor
P19474	-1.1365988	0.3417059	7.930483	-3.326248	0.0105730	0.0489788	E3 ubiquitin-protein ligase TRIM21
O75436	-0.9929865	0.3067959	8.751304	-3.236636	0.0105952	0.0489788	Vacuolar protein sorting-associated protein 26A
Q08AG7	-1.1984106	0.3496044	7.161376	-3.427905	0.0106361	0.0490564	Mitotic-spindle organizing protein 1
Q8IWU2	-0.7035098	0.2137465	8.159580	-3.291327	0.0107028	0.0491840	Serine/threonine-protein kinase LMTK2
Q8IWB7	1.6050991	0.4816712	7.808945	3.332354	0.0107121	0.0491840	WD repeat and FYVE domain-containing protein 1
Q0VAK6	1.1733962	0.3606850	8.492777	3.253244	0.0107427	0.0492132	Leiomodin-3
P07196	-3.1402185	0.8492355	5.757771	-3.697701	0.0108927	0.0497880	Neurofilament light polypeptide

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 
##                         0.5569921                         0.6129645 
## tissueV + 0.5 * locationR:tissueV                 locationR:tissueV 
##                         0.4130252                         0.8304050

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,]