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

colData(pe)$compartment <- paste0(colData(pe)$location,colData(pe)$tissue) %>% 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 = ~ compartment + patient)

4.2 Inference

Explore Design

library(ExploreModelMatrix)
VisualizeDesign(colData(pe),~ compartment + patient)$plotlist
## [[1]]

\[ \begin{array}{ccl} y_i &=& \beta_0 + \beta_{RA}x_{RA,i} + \beta_{LV}x_{LV,i} + \beta_{RV}x_{VR,i} +\beta_{p4}x_{p4,i} + \beta_{p8}x_{p8,i} + \epsilon_i\\ \epsilon_i&\sim& N(0, \sigma^2) \end{array} \] Means for patient “.”?

\[ \begin{array}{ccc} \mu^{LA}_. &=& \beta_0 + \beta_{p.}\\ \mu^{RA}_. &=& \beta_0 + \beta_{RA}+ \beta_{p.}\\ \mu^{LV}_. &=& \beta_0 + \beta_{LV}+ \beta_{p.}\\ \mu^{RV}_. &=& \beta_0 + \beta_{RV}+ \beta_{p.} \end{array} \]

\(\log_2\) FC after correcting for patient?

\[ \begin{array}{lcc} \log_2 \text{FC}_{V-A}^L &=& \beta_{LV}\\ \log_2 \text{FC}_{V-A}^R &=& \beta_{RV} - \beta_{RA}\\ \log_2 \text{FC}_{V-R}^{AVG} &=& \frac{1}{2}\beta_{LV} + \frac{1}{2} \beta_{RV} - \frac{1}{2} \beta_{RA}\\ \log_2 \text{FC}_{V-A}^R - \log \text{FC}_{V-A}^L &=& \beta_{RV} - \beta_{RA} - \beta_{LV}\\ \log_2 \text{FC}_{LA-1/3(LV+RA+RV)} &=& - \frac{1}{3}\beta_{LV} - \frac{1}{3}\beta_{RV} - \frac{1}{3}\beta_{RA} \end{array} \]

design <- model.matrix(~compartment + patient, data = colData(pe))
L <- makeContrast(
  c(
    "compartmentLV = 0",
    "compartmentRV-compartmentRA = 0",
    "1/2*compartmentLV+1/2*compartmentRV - 1/2 *compartmentRA = 0",
    "compartmentRV-compartmentRA - compartmentLV  = 0",
     "- 1/3*compartmentLV - 1/3*compartmentRV - 1/3*compartmentRA = 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"]])$"compartmentLV",
                 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"]])$"compartmentLV" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesLeft, ])

There are 195 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"compartmentLV" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval)  %>%
  knitr::kable(.)
logFC se df t pval adjPval rowData(pe[[“proteinRobust”]])$Protein.names
P08590 7.9679512 0.4400941 9.340284 18.105107 0.0000000 0.0000283 Myosin light chain 3
P12883 4.6698827 0.3746617 9.154805 12.464267 0.0000005 0.0004906 Myosin-7
P10916 6.9261087 0.5329054 7.340284 12.996882 0.0000025 0.0017099 Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q6UWY5 -3.2536428 0.3858890 9.086398 -8.431551 0.0000137 0.0054161 Olfactomedin-like protein 1
O75368 -2.2715945 0.2751679 9.262397 -8.255302 0.0000144 0.0054161 SH3 domain-binding glutamic acid-rich-like protein
P46821 -2.1668803 0.2669152 9.340284 -8.118235 0.0000157 0.0054161 Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
O95865 -2.1732192 0.2860790 9.340284 -7.596570 0.0000272 0.0072708 N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q8N474 -3.3090235 0.3840371 7.870618 -8.616415 0.0000282 0.0072708 Secreted frizzled-related protein 1
Q9ULL5-3 -3.4165405 0.4032200 7.819264 -8.473144 0.0000330 0.0075808 Proline-rich protein 12
P21810 -3.2145420 0.4247335 8.729933 -7.568373 0.0000406 0.0077545 Biglycan
P14854 2.4019126 0.3094122 8.404606 7.762825 0.0000413 0.0077545 Cytochrome c oxidase subunit 6B1
O94875-10 2.3744000 0.3219457 8.878050 7.375156 0.0000453 0.0077953 Sorbin and SH3 domain-containing protein 2
P05546 -1.9318824 0.2735967 9.244798 -7.061058 0.0000516 0.0082019 Heparin cofactor 2
P29622 -2.1134793 0.3046411 9.340284 -6.937605 0.0000564 0.0083202 Kallistatin
Q16647 -2.7991521 0.3992411 9.001381 -7.011182 0.0000624 0.0085937 Prostacyclin synthase
P02452 -2.9630153 0.4032446 8.265405 -7.347936 0.0000677 0.0087410 Collagen alpha-1(I) chain
P51884 -2.1343314 0.3193365 9.130509 -6.683644 0.0000843 0.0102416 Lumican
Q8TBQ9 -2.8189960 0.4093554 8.596029 -6.886428 0.0000896 0.0102821 Protein kish-A
P36955 -2.3377901 0.3391640 8.116692 -6.892802 0.0001171 0.0105721 Pigment epithelium-derived factor
P07451 -1.8489373 0.2930212 9.340284 -6.309909 0.0001186 0.0105721 Carbonic anhydrase 3
P00325 -2.1119462 0.3268927 8.957138 -6.460671 0.0001192 0.0105721 Alcohol dehydrogenase 1B
Q9UBG0 -2.5547510 0.4003554 9.145533 -6.381207 0.0001193 0.0105721 C-type mannose receptor 2
P24844 -2.4962161 0.3958181 9.285071 -6.306472 0.0001222 0.0105721 Myosin regulatory light polypeptide 9
P23083 -4.2325442 0.5769131 7.340284 -7.336536 0.0001249 0.0105721 Ig heavy chain V-I region V35
Q15113 -2.7424988 0.4354793 9.158959 -6.297656 0.0001311 0.0105721 Procollagen C-endopeptidase enhancer 1
P51888 -3.0081810 0.4052399 7.132475 -7.423211 0.0001335 0.0105721 Prolargin
Q06828 -4.2030186 0.6647241 8.942141 -6.322952 0.0001411 0.0105721 Fibromodulin
Q53GQ0 -2.4232423 0.3933995 9.330707 -6.159749 0.0001434 0.0105721 Very-long-chain 3-oxoacyl-CoA reductase
P13533 -4.0404076 0.6506338 9.071511 -6.209956 0.0001518 0.0108102 Myosin-6
P35442 -2.3010500 0.3554251 8.340284 -6.474078 0.0001611 0.0110879 Thrombospondin-2
P08294 -2.7503241 0.4291604 7.934754 -6.408615 0.0002146 0.0141612 Extracellular superoxide dismutase [Cu-Zn]
Q96LL9 -2.4127080 0.4014527 8.730254 -6.009944 0.0002261 0.0141612 DnaJ homolog subfamily C member 30
P18428 -1.9996058 0.3416979 9.111796 -5.851970 0.0002318 0.0141612 Lipopolysaccharide-binding protein
P36021 -3.1085951 0.5065411 8.340284 -6.136906 0.0002346 0.0141612 Monocarboxylate transporter 8
Q9UL18 -2.6225313 0.4127027 7.833453 -6.354529 0.0002400 0.0141612 Protein argonaute-1
Q92508 4.0552373 0.5615051 6.340284 7.222085 0.0002775 0.0157864 Piezo-type mechanosensitive ion channel component 1
P46060 -1.9620904 0.3294260 8.340284 -5.956088 0.0002887 0.0157864 Ran GTPase-activating protein 1
P02743 -2.1700557 0.3876106 9.340284 -5.598546 0.0002927 0.0157864 Serum amyloid P-component;Serum amyloid P-component(1-203)
Q9UGT4 -2.3006162 0.4106218 9.164961 -5.602762 0.0003118 0.0157864 Sushi domain-containing protein 2
P05997 -3.0856148 0.5432268 8.913310 -5.680160 0.0003128 0.0157864 Collagen alpha-2(V) chain
Q14764 -1.6267934 0.2932870 9.340284 -5.546762 0.0003134 0.0157864 Major vault protein
Q8WWA0 -5.8725166 0.9903431 8.075941 -5.929780 0.0003373 0.0163611 Intelectin-1
O60760 -3.5990151 0.6245474 8.340284 -5.762597 0.0003621 0.0163611 Hematopoietic prostaglandin D synthase
O43677 -2.7199107 0.4742575 8.403733 -5.735092 0.0003637 0.0163611 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q9BW30 -2.7245919 0.4917306 8.972354 -5.540822 0.0003646 0.0163611 Tubulin polymerization-promoting protein family member 3
Q9P2B2 -2.0393915 0.3758580 9.340284 -5.425962 0.0003682 0.0163611 Prostaglandin F2 receptor negative regulator
P40261 -2.3445730 0.4296756 9.193837 -5.456612 0.0003734 0.0163611 Nicotinamide N-methyltransferase
Q9UBB5 2.7451793 0.4017040 6.340284 6.833837 0.0003803 0.0163611 Methyl-CpG-binding domain protein 2
Q9NZ01 -2.4109216 0.4391203 8.605914 -5.490344 0.0004503 0.0182951 Very-long-chain enoyl-CoA reductase
P00748 -1.9914680 0.3724325 9.076240 -5.347192 0.0004511 0.0182951 Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q92736-2 -3.3064395 0.6067354 8.686628 -5.449558 0.0004589 0.0182951 Ryanodine receptor 2
O14967 -2.3785961 0.4319466 8.500434 -5.506690 0.0004607 0.0182951 Calmegin
O00180 -4.2526703 0.7693187 8.340284 -5.527840 0.0004799 0.0186298 Potassium channel subfamily K member 1
P12110 -1.9881397 0.3565898 8.142157 -5.575425 0.0004934 0.0186298 Collagen alpha-2(VI) chain
Q07954 -1.6573532 0.3183411 9.340284 -5.206219 0.0004962 0.0186298 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 0.4587217 8.119643 -5.510510 0.0005382 0.0198447 Reversion-inducing cysteine-rich protein with Kazal motifs
P31994-2 -1.5795166 0.3050599 9.042192 -5.177726 0.0005725 0.0207342 Low affinity immunoglobulin gamma Fc region receptor II-b
O00264 -1.9731043 0.3815307 9.017305 -5.171548 0.0005824 0.0207342 Membrane-associated progesterone receptor component 1
Q8TBP6 -1.9233155 0.3729737 8.951972 -5.156706 0.0006080 0.0209469 Solute carrier family 25 member 40
Q14195-2 -2.5380012 0.4984603 9.203313 -5.091681 0.0006086 0.0209469 Dihydropyrimidinase-related protein 3
Q8WZA9 -1.4960398 0.2950487 9.151176 -5.070483 0.0006377 0.0215099 Immunity-related GTPase family Q protein
Q9BXN1 -2.6634064 0.5205230 8.932248 -5.116789 0.0006458 0.0215099 Asporin
O43464 -1.9028432 0.3781327 9.086623 -5.032209 0.0006869 0.0225141 Serine protease HTRA2, mitochondrial
P01699 -4.3035389 0.6943613 6.221815 -6.197838 0.0007076 0.0225572 Ig lambda chain V-I region VOR
Q9GZY4 -3.1557642 0.5814512 7.695874 -5.427393 0.0007130 0.0225572 Cytochrome c oxidase assembly factor 1 homolog
P41240 -1.5466953 0.3081175 8.970235 -5.019823 0.0007265 0.0225572 Tyrosine-protein kinase CSK
P06858 1.7891922 0.3611605 9.222404 4.954009 0.0007319 0.0225572 Lipoprotein lipase
Q9NVN8 -6.0616246 0.8809255 5.340284 -6.880973 0.0007588 0.0230436 Guanine nucleotide-binding protein-like 3-like protein
P04083 -1.5201990 0.3119422 9.340284 -4.873336 0.0007900 0.0233152 Annexin A1
Q8NAT1 -1.3792038 0.2822718 9.280761 -4.886085 0.0007903 0.0233152 Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
P02747 -2.6697776 0.4746685 6.963608 -5.624510 0.0008099 0.0233355 Complement C1q subcomponent subunit C
O95631 -3.9795086 0.5866855 5.340284 -6.783035 0.0008136 0.0233355 Netrin-1
Q92621 -1.7036447 0.3537154 9.337319 -4.816428 0.0008575 0.0239435 Nuclear pore complex protein Nup205
A6NMZ7 -2.2762344 0.4734404 9.340284 -4.807859 0.0008673 0.0239435 Collagen alpha-6(VI) chain
Q9NY15 -2.1436460 0.4457105 9.323614 -4.809503 0.0008696 0.0239435 Stabilin-1
P02775 -1.9622566 0.4098267 9.340284 -4.788015 0.0008923 0.0242383 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 0.4704068 9.272310 -4.784054 0.0009159 0.0242383 Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
Q96C86 -1.4762676 0.3061798 9.069123 -4.821570 0.0009246 0.0242383 m7GpppX diphosphatase
O14980 -1.2169774 0.2556030 9.340284 -4.761203 0.0009273 0.0242383 Exportin-1
P48681 -1.3334013 0.2816825 9.337319 -4.733703 0.0009656 0.0249234 Nestin
Q9UNW9 4.0122337 0.8582727 9.062101 4.674777 0.0011395 0.0282152 RNA-binding protein Nova-2
P24311 1.7937075 0.3894249 9.340284 4.606042 0.0011610 0.0282152 Cytochrome c oxidase subunit 7B, mitochondrial
P50552 -1.5288544 0.3264365 8.956759 -4.683467 0.0011616 0.0282152 Vasodilator-stimulated phosphoprotein
Q53GG5-2 -2.9088697 0.6043809 8.329769 -4.812974 0.0011899 0.0282152 PDZ and LIM domain protein 3
Q8WY22 -1.8091979 0.3762334 8.340284 -4.808712 0.0011924 0.0282152 BRI3-binding protein
Q7L4S7 -1.7124303 0.3284737 7.072977 -5.213294 0.0011953 0.0282152 Protein ARMCX6
P49207 -1.5105253 0.3238981 8.944352 -4.663581 0.0011990 0.0282152 60S ribosomal protein L34
P56539 -2.0161968 0.4237538 8.518982 -4.757944 0.0012024 0.0282152 Caveolin-3
P46063 -1.3496984 0.2923380 9.103089 -4.616911 0.0012227 0.0282250 ATP-dependent DNA helicase Q1
Q5M9N0 -3.5146838 0.7340509 8.305567 -4.788065 0.0012396 0.0282250 Coiled-coil domain-containing protein 158
Q6SZW1 -2.6395602 0.5225610 7.340284 -5.051201 0.0012816 0.0282250 Sterile alpha and TIR motif-containing protein 1
Q5NDL2 -2.2948242 0.4905128 8.637646 -4.678419 0.0012899 0.0282250 EGF domain-specific O-linked N-acetylglucosamine transferase
P02671 -2.1346012 0.3897245 6.337319 -5.477206 0.0012935 0.0282250 Fibrinogen alpha chain;Fibrinopeptide A;Fibrinogen alpha chain
Q9BXR6 -2.3571850 0.5203072 9.337319 -4.530372 0.0012981 0.0282250 Complement factor H-related protein 5
Q9HAV4 -2.4188578 0.4880665 7.590421 -4.956000 0.0012985 0.0282250 Exportin-5
Q92681 -2.1962163 0.4532791 7.852261 -4.845174 0.0013493 0.0290237 Regulatory solute carrier protein family 1 member 1
Q8TDB6 -1.7610737 0.3867549 9.021971 -4.553462 0.0013705 0.0291445 E3 ubiquitin-protein ligase DTX3L
Q96H79 -3.2031583 0.5804766 6.120849 -5.518153 0.0013947 0.0291445 Zinc finger CCCH-type antiviral protein 1-like
O15230 -1.4246624 0.3079349 8.609473 -4.626505 0.0013972 0.0291445 Laminin subunit alpha-5
Q15274 -1.9285076 0.4038904 7.836023 -4.774830 0.0014827 0.0303670 Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Q9BUF5 -1.9157084 0.4299634 9.220990 -4.455515 0.0014953 0.0303670 Tubulin beta-6 chain
Q9Y5U8 -4.0913780 0.9204171 9.239505 -4.445135 0.0015108 0.0303670 Mitochondrial pyruvate carrier 1
P14550 -1.3982496 0.3084731 8.775886 -4.532808 0.0015147 0.0303670 Alcohol dehydrogenase [NADP(+)]
O15111 -1.9484725 0.3865527 6.876283 -5.040639 0.0015770 0.0313123 Inhibitor of nuclear factor kappa-B kinase subunit alpha
Q12996 -2.0094808 0.3846419 6.413766 -5.224289 0.0016030 0.0313127 Cleavage stimulation factor subunit 3
O75828 -1.6544202 0.3779045 9.340284 -4.377879 0.0016259 0.0313127 Carbonyl reductase [NADPH] 3
P06727 -1.3683135 0.3051631 8.760880 -4.483875 0.0016299 0.0313127 Apolipoprotein A-IV
Q9UBI9 -2.9866384 0.6097023 7.151144 -4.898519 0.0016520 0.0313127 Headcase protein homolog
P04196 -1.9303128 0.4014882 7.426268 -4.807895 0.0016528 0.0313127 Histidine-rich glycoprotein
Q9ULC3 -1.6333020 0.3657301 8.640607 -4.465867 0.0017303 0.0324820 Ras-related protein Rab-23
P01031 -1.3157564 0.2935518 8.464855 -4.482196 0.0017802 0.0326157 Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q6ZSY5 -1.6890696 0.3884148 9.155821 -4.348623 0.0017804 0.0326157 Protein phosphatase 1 regulatory subunit 3F
P02461 -3.6062939 0.7999724 8.336698 -4.508023 0.0017854 0.0326157 Collagen alpha-1(III) chain
P14555 -4.6109150 0.9340518 6.836488 -4.936466 0.0018006 0.0326157 Phospholipase A2, membrane associated
Q8N5M1 -1.9899041 0.4583963 9.042872 -4.341012 0.0018538 0.0331599 ATP synthase mitochondrial F1 complex assembly factor 2
P04003 -1.5009188 0.3445982 8.942972 -4.355561 0.0018631 0.0331599 C4b-binding protein alpha chain
P45877 -1.2442932 0.2906244 9.340284 -4.281448 0.0018788 0.0331599 Peptidyl-prolyl cis-trans isomerase C
P08582 -1.6911943 0.3960741 9.314743 -4.269894 0.0019238 0.0336658 Melanotransferrin
Q6YN16 1.5603531 0.3668238 9.340284 4.253686 0.0019591 0.0339967 Hydroxysteroid dehydrogenase-like protein 2
Q13636 -3.2633858 0.6378192 6.153571 -5.116475 0.0020274 0.0344599 Ras-related protein Rab-31
O75746 -1.5795706 0.3619821 8.572666 -4.363671 0.0020362 0.0344599 Calcium-binding mitochondrial carrier protein Aralar1
Q9UQ35 -1.3570787 0.3211094 9.321024 -4.226219 0.0020516 0.0344599 Serine/arginine repetitive matrix protein 2
P34932 -1.1578310 0.2728472 9.211678 -4.243514 0.0020526 0.0344599 Heat shock 70 kDa protein 4
Q5VIR6-4 -1.7638024 0.4156700 9.087145 -4.243275 0.0021173 0.0349863 Vacuolar protein sorting-associated protein 53 homolog
P04004 -1.6269790 0.3786641 8.705024 -4.296628 0.0021607 0.0349863 Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
Q9H1E5 -1.3852786 0.3312366 9.340284 -4.182142 0.0021834 0.0349863 Thioredoxin-related transmembrane protein 4
P02776 -1.7615098 0.3962447 7.949110 -4.445510 0.0021862 0.0349863 Platelet factor 4;Platelet factor 4, short form
Q8WWQ0 -1.6224614 0.3883304 9.340284 -4.178044 0.0021971 0.0349863 PH-interacting protein
P01042 -2.2103015 0.4771052 7.226305 -4.632734 0.0021987 0.0349863 Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
P04209 1.3436120 0.3189275 9.110306 4.212907 0.0022025 0.0349863 Ig lambda chain V-II region NIG-84
P15924 1.2648885 0.3036900 9.303671 4.165064 0.0022601 0.0356269 Desmoplakin
Q9BTV4 -1.8099873 0.4338399 9.131742 -4.172016 0.0023293 0.0361977 Transmembrane protein 43
Q2TAA5 -1.2916274 0.3101174 9.154381 -4.164963 0.0023414 0.0361977 GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
Q08945 -2.0204841 0.4692380 8.340284 -4.305884 0.0023553 0.0361977 FACT complex subunit SSRP1
Q53T59 -1.8461756 0.4216827 7.957563 -4.378116 0.0023849 0.0361977 HCLS1-binding protein 3
Q04721 1.5358466 0.3697229 9.133444 4.154048 0.0023920 0.0361977 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
P09619 -1.6085799 0.3879147 9.146538 -4.146737 0.0024109 0.0361977 Platelet-derived growth factor receptor beta
P05455 -1.2004499 0.2890383 9.091089 -4.153255 0.0024190 0.0361977 Lupus La protein
Q9Y6X5 -1.3875045 0.3282282 8.625019 -4.227255 0.0024376 0.0362127 Bis(5-adenosyl)-triphosphatase ENPP4
Q5JPH6 3.5281305 0.6900930 5.749214 5.112544 0.0024892 0.0367157 Probable glutamate–tRNA ligase, mitochondrial
O60262 -1.5577722 0.3701409 8.619942 -4.208592 0.0025071 0.0367171 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
O75348 -1.8591253 0.4550945 9.340284 -4.085141 0.0025320 0.0368207 V-type proton ATPase subunit G 1
O00303 -1.4561773 0.3529310 8.971112 -4.125955 0.0025928 0.0374408 Eukaryotic translation initiation factor 3 subunit F
P01034 -1.6978634 0.4102103 8.779058 -4.139007 0.0026644 0.0382077 Cystatin-C
P25940 -1.7454125 0.4287038 9.075544 -4.071372 0.0027456 0.0389422 Collagen alpha-3(V) chain
P49458 -2.2735269 0.5093390 7.171760 -4.463681 0.0027533 0.0389422 Signal recognition particle 9 kDa protein
P62760 -1.9146688 0.4724484 9.079691 -4.052652 0.0028216 0.0396362 Visinin-like protein 1
Q14019 -3.9129083 0.8381911 6.340284 -4.668277 0.0029759 0.0415222 Coactosin-like protein
O15116 -3.2231772 0.6547793 5.714555 -4.922540 0.0030377 0.0415506 U6 snRNA-associated Sm-like protein LSm1
P08311 -1.3139510 0.3247423 8.802163 -4.046134 0.0030380 0.0415506 Cathepsin G
Q9UKS6 1.4372286 0.3567265 8.911835 4.028937 0.0030383 0.0415506 Protein kinase C and casein kinase substrate in neurons protein 3
Q9UKX3 2.1517579 0.5397244 9.158347 3.986771 0.0030643 0.0415977 Myosin-13
P30405 -1.5177122 0.3834871 9.340284 -3.957661 0.0030821 0.0415977 Peptidyl-prolyl cis-trans isomerase F, mitochondrial
P36551 -1.3202398 0.3300771 8.998694 -3.999792 0.0031123 0.0417333 Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial
Q9Y2Z0 -1.7414076 0.4413324 9.340284 -3.945796 0.0031393 0.0418240 Suppressor of G2 allele of SKP1 homolog
P19429 2.3063639 0.5595520 8.131116 4.121805 0.0032212 0.0426396 Troponin I, cardiac muscle
P54577 -1.3002728 0.3270699 8.936604 -3.975520 0.0032734 0.0430546 Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
P54652 -1.5932853 0.4038428 9.051681 -3.945310 0.0033409 0.0436640 Heat shock-related 70 kDa protein 2
O75475 -1.9038879 0.4864336 9.212925 -3.913973 0.0033869 0.0439871 PC4 and SFRS1-interacting protein
Q7LBR1 -2.8413335 0.7340608 9.340284 -3.870706 0.0035288 0.0453429 Charged multivesicular body protein 1b
P25311 -1.5051007 0.3767094 8.476167 -3.995389 0.0035352 0.0453429 Zinc-alpha-2-glycoprotein
P60468 -1.4647431 0.3637423 8.195483 -4.026870 0.0036199 0.0461421 Protein transport protein Sec61 subunit beta
Q04941 -1.9356392 0.4977255 9.042111 -3.888969 0.0036481 0.0461851 Proteolipid protein 2
Q9BS26 -1.2463986 0.3233735 9.274757 -3.854362 0.0036680 0.0461851 Endoplasmic reticulum resident protein 44
P03950 -2.2030636 0.5479121 8.125070 -4.020834 0.0037162 0.0465092 Angiogenin
Q1KMD3 -1.4744120 0.3808495 8.985347 -3.871377 0.0037925 0.0471361 Heterogeneous nuclear ribonucleoprotein U-like protein 2
Q13641 -2.2297004 0.5261897 7.031795 -4.237446 0.0038131 0.0471361 Trophoblast glycoprotein
P26447 -1.8372154 0.4700925 8.678479 -3.908200 0.0038348 0.0471361 Protein S100-A4
Q96PK6 -1.3089284 0.3409020 9.038611 -3.839604 0.0039374 0.0481113 RNA-binding protein 14
O00567 -2.4335450 0.6393981 9.265594 -3.805994 0.0039627 0.0481351 Nucleolar protein 56
Q9Y3B4 -1.2603707 0.3293029 8.988346 -3.827390 0.0040536 0.0484443 Splicing factor 3B subunit 6
P12814 -1.6827515 0.4252653 8.129780 -3.956945 0.0040623 0.0484443 Alpha-actinin-1
Q86VU5 1.5583619 0.4123883 9.340284 3.778870 0.0040754 0.0484443 Catechol O-methyltransferase domain-containing protein 1
Q13478 -1.6083281 0.4196718 8.918034 -3.832347 0.0040820 0.0484443 Interleukin-18 receptor 1
P01024 -1.1180307 0.2942775 9.077710 -3.799239 0.0041567 0.0487898 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
Q9HB40 -2.1393191 0.4879364 6.281185 -4.384422 0.0041672 0.0487898 Retinoid-inducible serine carboxypeptidase
P01008 -1.5692162 0.4165458 9.296494 -3.767211 0.0041858 0.0487898 Antithrombin-III
P07384 -1.1052065 0.2928965 9.221341 -3.773369 0.0042062 0.0487898 Calpain-1 catalytic subunit
P14543 -1.4365423 0.3791734 9.073226 -3.788616 0.0042292 0.0487898 Nidogen-1
Q14011 -2.3803571 0.6106790 8.207070 -3.897886 0.0043378 0.0490195 Cold-inducible RNA-binding protein
Q7Z3T8 -1.6269924 0.4227501 8.506070 -3.848591 0.0043523 0.0490195 Zinc finger FYVE domain-containing protein 16
O94919 -1.1247209 0.2986523 9.104029 -3.765988 0.0043534 0.0490195 Endonuclease domain-containing 1 protein
O95486 -1.7001274 0.4499244 8.998127 -3.778696 0.0043594 0.0490195 Protein transport protein Sec24A
Q9UK22 -1.8807802 0.4351354 6.332093 -4.322287 0.0043857 0.0490195 F-box only protein 2
Q9Y2D4 -2.0300937 0.5313394 8.642469 -3.820710 0.0044034 0.0490195 Exocyst complex component 6B
P07357 -1.1425305 0.3049131 9.182819 -3.747069 0.0044153 0.0490195 Complement component C8 alpha chain
Q96ST3 -1.6077298 0.4273979 9.026590 -3.761669 0.0044500 0.0491401 Paired amphipathic helix protein Sin3a
Q9BXY0 -1.9170100 0.4411685 6.200292 -4.345301 0.0044887 0.0493042 Protein MAK16 homolog
Q9BVC6 -1.6329609 0.4400488 9.340284 -3.710863 0.0045371 0.0493121 Transmembrane protein 109
P09467 -2.0219103 0.4982196 7.193752 -4.058271 0.0045513 0.0493121 Fructose-1,6-bisphosphatase 1
P56199 -1.2716373 0.3341871 8.563613 -3.805166 0.0045836 0.0493121 Integrin alpha-1
P51665 -1.2958979 0.3484749 9.217447 -3.718769 0.0045849 0.0493121 26S proteasome non-ATPase regulatory subunit 7
P50991 -1.7929240 0.4684315 8.384169 -3.827505 0.0046125 0.0493449 T-complex protein 1 subunit delta
O43143 -0.9916403 0.2683632 9.340284 -3.695143 0.0046515 0.0493449 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
Q6IC98 -1.1710653 0.3087962 8.575771 -3.792356 0.0046597 0.0493449 GRAM domain-containing protein 4

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

4.4.1 Volcano-plot

volcanoRight <- ggplot(rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA",
                 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"]])$"compartmentRV - compartmentRA" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesRight, ])

There are 78 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA"  %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)
logFC se df t pval adjPval rowData(pe[[“proteinRobust”]])$Protein.names
P08590 5.503838 0.4400941 9.340284 12.506047 0.0000004 0.0008111 Myosin light chain 3
P06858 3.354674 0.3574485 9.222404 9.385056 0.0000051 0.0054051 Lipoprotein lipase
Q9ULD0 -3.575906 0.3784428 7.340284 -9.449003 0.0000229 0.0161924 2-oxoglutarate dehydrogenase-like, mitochondrial
P35442 -3.246460 0.4104096 8.340284 -7.910294 0.0000375 0.0167832 Thrombospondin-2
P02776 -2.818363 0.3456939 7.949110 -8.152772 0.0000395 0.0167832 Platelet factor 4;Platelet factor 4, short form
P21810 -2.924783 0.4110720 8.729933 -7.115013 0.0000651 0.0221578 Biglycan
O75368 -1.819326 0.2733282 9.262397 -6.656196 0.0000814 0.0221578 SH3 domain-binding glutamic acid-rich-like protein
A6NMZ7 -3.070848 0.4734404 9.340284 -6.486239 0.0000958 0.0221578 Collagen alpha-6(VI) chain
P54652 -2.726681 0.4146013 9.051681 -6.576635 0.0000993 0.0221578 Heat shock-related 70 kDa protein 2
Q6UWY5 -2.456874 0.3768643 9.086398 -6.519254 0.0001044 0.0221578 Olfactomedin-like protein 1
Q06828 -4.122091 0.6387887 8.942141 -6.452980 0.0001212 0.0232317 Fibromodulin
P05546 -1.727800 0.2758735 9.244798 -6.263016 0.0001313 0.0232317 Heparin cofactor 2
P28066 -2.176824 0.3418310 8.702920 -6.368129 0.0001506 0.0237191 Proteasome subunit alpha type-5
P29622 -1.847919 0.3046411 9.340284 -6.065891 0.0001605 0.0237191 Kallistatin
P46821 -1.606539 0.2669152 9.340284 -6.018910 0.0001702 0.0237191 Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P13533 -3.888317 0.6399941 9.071511 -6.075551 0.0001788 0.0237191 Myosin-6
Q9UGT4 -2.443145 0.4171457 9.164961 -5.856815 0.0002252 0.0269952 Sushi domain-containing protein 2
P35625 -3.938312 0.6193484 7.913419 -6.358798 0.0002289 0.0269952 Metalloproteinase inhibitor 3
Q69YU5 3.254738 0.5585046 8.668560 5.827594 0.0002895 0.0294312 Uncharacterized protein C12orf73
Q6PCB0 -2.328852 0.4064258 8.907178 -5.730079 0.0002946 0.0294312 von Willebrand factor A domain-containing protein 1
O43677 -2.969964 0.5093818 8.403733 -5.830526 0.0003247 0.0294312 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q15327 -2.203003 0.3964916 9.209552 -5.556241 0.0003256 0.0294312 Ankyrin repeat domain-containing protein 1
P60468 -2.438022 0.4150612 8.195483 -5.873887 0.0003397 0.0294312 Protein transport protein Sec61 subunit beta
Q14764 -1.608232 0.2932870 9.340284 -5.483475 0.0003409 0.0294312 Major vault protein
P01031 -1.626524 0.2853512 8.464855 -5.700077 0.0003693 0.0294312 Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q9P2B2 -2.035226 0.3758580 9.340284 -5.414879 0.0003737 0.0294312 Prostaglandin F2 receptor negative regulator
Q92930 -2.833666 0.4701862 7.581882 -6.026688 0.0003877 0.0294312 Ras-related protein Rab-8B
P02775 -2.205543 0.4098267 9.340284 -5.381647 0.0003908 0.0294312 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 0.4924404 7.544947 -6.010331 0.0004020 0.0294312 NADP-dependent malic enzyme
P12883 1.969100 0.3684373 9.154805 5.344464 0.0004397 0.0302160 Myosin-7
P48681 -1.491288 0.2817522 9.337319 -5.292906 0.0004412 0.0302160 Nestin
P11586 2.013301 0.3561932 7.968800 5.652272 0.0004870 0.0323074 C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
P30711 -2.321740 0.4510188 9.010502 -5.147768 0.0006027 0.0375765 Glutathione S-transferase theta-1
Q9BZH6 3.442805 0.6446423 8.293516 5.340645 0.0006153 0.0375765 WD repeat-containing protein 11
Q9UHG2 -3.175806 0.6135214 8.817237 -5.176356 0.0006216 0.0375765 ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
Q9H1K0 -2.237374 0.3942172 7.340284 -5.675485 0.0006372 0.0375765 Rabenosyn-5
P00748 -1.915326 0.3817571 9.076240 -5.017133 0.0007037 0.0390894 Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
Q5NDL2 -2.708130 0.5283924 8.637646 -5.125224 0.0007094 0.0390894 EGF domain-specific O-linked N-acetylglucosamine transferase
O00180 -4.621308 0.8883327 8.340284 -5.202227 0.0007181 0.0390894 Potassium channel subfamily K member 1
P23142 -2.779235 0.5118492 7.508971 -5.429792 0.0007724 0.0394842 Fibulin-1
P10916 2.921175 0.5329054 7.340284 5.481602 0.0007872 0.0394842 Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q00G26 1.964123 0.3638881 7.523732 5.397602 0.0007959 0.0394842 Perilipin-5
Q09161 2.370716 0.3923646 6.133648 6.042126 0.0008569 0.0394842 Nuclear cap-binding protein subunit 1
Q9BW30 -2.326597 0.4750319 8.972354 -4.897769 0.0008579 0.0394842 Tubulin polymerization-promoting protein family member 3
P30405 -1.842938 0.3834871 9.340284 -4.805736 0.0008699 0.0394842 Peptidyl-prolyl cis-trans isomerase F, mitochondrial
P18428 -1.690875 0.3486074 9.111796 -4.850370 0.0008763 0.0394842 Lipopolysaccharide-binding protein
Q9NRG4 2.622493 0.5207932 8.340284 5.035575 0.0008877 0.0394842 N-lysine methyltransferase SMYD2
Q5JPH6 3.287773 0.5234533 5.749214 6.280929 0.0008927 0.0394842 Probable glutamate–tRNA ligase, mitochondrial
Q9BUH6 -1.485484 0.3099762 9.116217 -4.792253 0.0009495 0.0411371 Protein PAXX
P35052 -1.965366 0.3825553 7.767251 -5.137469 0.0009735 0.0413337 Glypican-1;Secreted glypican-1
O15061 -1.710970 0.3633241 9.340284 -4.709210 0.0009994 0.0416033 Synemin
P08603 -1.484314 0.3180017 9.340284 -4.667629 0.0010614 0.0428621 Complement factor H
Q96FN9 -2.712489 0.5578954 8.340284 -4.862004 0.0011118 0.0428621 Probable D-tyrosyl-tRNA(Tyr) deacylase 2
Q04760 2.254328 0.4736692 8.703014 4.759288 0.0011312 0.0428621 Lactoylglutathione lyase
Q96KC8 -2.480944 0.5091790 8.228142 -4.872440 0.0011402 0.0428621 DnaJ homolog subfamily C member 1
Q8N474 -2.108536 0.4246499 7.870618 -4.965352 0.0011538 0.0428621 Secreted frizzled-related protein 1
P04004 -1.908509 0.4030954 8.705024 -4.734634 0.0011693 0.0428621 Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
Q99983 -3.527403 0.6633634 6.869856 -5.317452 0.0011710 0.0428621 Osteomodulin
P24298 1.991397 0.4217496 8.561120 4.721751 0.0012456 0.0448202 Alanine aminotransferase 1
P62857 -2.074531 0.4193083 7.633329 -4.947508 0.0012904 0.0456583 40S ribosomal protein S28
P23434 1.406476 0.3118008 9.340284 4.510817 0.0013350 0.0464610 Glycine cleavage system H protein, mitochondrial
P24844 -1.767461 0.3939584 9.285071 -4.486415 0.0014045 0.0480939 Myosin regulatory light polypeptide 9
Q6PI78 1.975693 0.4409304 9.012099 4.480736 0.0015257 0.0489943 Transmembrane protein 65
P04275 -1.352764 0.3022121 8.915943 -4.476206 0.0015772 0.0489943 von Willebrand factor;von Willebrand antigen 2
Q15113 -1.959899 0.4426566 9.158959 -4.427583 0.0015838 0.0489943 Procollagen C-endopeptidase enhancer 1
P01611 -2.213481 0.5044273 9.340284 -4.388107 0.0016013 0.0489943 Ig kappa chain V-I region Wes
Q9BSD7 2.993219 0.6127958 7.126859 4.884530 0.0016954 0.0489943 Cancer-related nucleoside-triphosphatase
P04350 -2.861432 0.5769202 6.912964 -4.959840 0.0016986 0.0489943 Tubulin beta-4A chain
Q86WV6 -1.310297 0.2996647 9.195764 -4.372543 0.0017009 0.0489943 Stimulator of interferon genes protein
O75204 -2.010330 0.3875241 6.340284 -5.187626 0.0017240 0.0489943 Transmembrane protein 127
P51888 -1.838614 0.3781273 7.132475 -4.862421 0.0017356 0.0489943 Prolargin
Q6UWS5 1.798858 0.3720055 7.211958 4.835568 0.0017359 0.0489943 Protein PET117 homolog, mitochondrial
P08294 -1.884866 0.4078093 7.934754 -4.621931 0.0017430 0.0489943 Extracellular superoxide dismutase [Cu-Zn]
Q9UL26 7.763006 1.7542223 8.794843 4.425326 0.0017543 0.0489943 Ras-related protein Rab-22A
P82663 -1.944516 0.4491714 9.292843 -4.329117 0.0017699 0.0489943 28S ribosomal protein S25, mitochondrial
P01303 -2.151374 0.4894477 8.910350 -4.395514 0.0017739 0.0489943 Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
Q7L4S7 -2.514619 0.5171422 7.072977 -4.862529 0.0017770 0.0489943 Protein ARMCX6
P50453 -1.398216 0.3198649 8.918514 -4.371271 0.0018331 0.0498931 Serpin B9

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

4.5.1 Volcano-plot

volcanoAvg <- ggplot(rowData(pe[["proteinRobust"]])$"1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA",
                 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"]])$"1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesAvg, ])

There are 435 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)
logFC se df t pval adjPval rowData(pe[[“proteinRobust”]])$Protein.names
P08590 6.7358945 0.3111935 9.340284 21.645354 0.0000000 0.0000054 Myosin light chain 3
P12883 3.3194914 0.2627344 9.154805 12.634401 0.0000004 0.0004295 Myosin-7
O75368 -2.0454601 0.1939237 9.262397 -10.547755 0.0000018 0.0007869 SH3 domain-binding glutamic acid-rich-like protein
P10916 4.9236420 0.3687164 7.340284 13.353466 0.0000021 0.0007869 Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
Q6UWY5 -2.8552584 0.2696929 9.086398 -10.587074 0.0000021 0.0007869 Olfactomedin-like protein 1
P06858 2.5719330 0.2540700 9.222404 10.122931 0.0000027 0.0007869 Lipoprotein lipase
P46821 -1.8867094 0.1887375 9.340284 -9.996471 0.0000027 0.0007869 Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1
P21810 -3.0696624 0.2952449 8.729933 -10.397005 0.0000033 0.0008330 Biglycan
P05546 -1.8298412 0.1942687 9.244798 -9.419125 0.0000049 0.0010236 Heparin cofactor 2
P35442 -2.7737551 0.2714604 8.340284 -10.217899 0.0000053 0.0010236 Thrombospondin-2
P29622 -1.9806994 0.2154138 9.340284 -9.194860 0.0000055 0.0010236 Kallistatin
Q06828 -4.1625547 0.4609526 8.942141 -9.030331 0.0000087 0.0014706 Fibromodulin
P13533 -3.9643622 0.4562478 9.071511 -8.689054 0.0000108 0.0016904 Myosin-6
Q8N474 -2.7087798 0.2848474 7.870618 -9.509584 0.0000138 0.0020020 Secreted frizzled-related protein 1
Q9UGT4 -2.3718806 0.2926691 9.164961 -8.104309 0.0000179 0.0021835 Sushi domain-containing protein 2
A6NMZ7 -2.6735410 0.3347729 9.340284 -7.986133 0.0000180 0.0021835 Collagen alpha-6(VI) chain
O95865 -1.5898713 0.2022884 9.340284 -7.859429 0.0000206 0.0021835 N(G),N(G)-dimethylarginine dimethylaminohydrolase 2
Q14764 -1.6175126 0.2073852 9.340284 -7.799556 0.0000219 0.0021835 Major vault protein
O94875-10 1.8826268 0.2329150 8.878050 8.082890 0.0000221 0.0021835 Sorbin and SH3 domain-containing protein 2
P02776 -2.2899367 0.2629231 7.949110 -8.709532 0.0000245 0.0021835 Platelet factor 4;Platelet factor 4, short form
Q9P2B2 -2.0373086 0.2657718 9.340284 -7.665632 0.0000252 0.0021835 Prostaglandin F2 receptor negative regulator
P24844 -2.1318385 0.2792289 9.285071 -7.634733 0.0000270 0.0021835 Myosin regulatory light polypeptide 9
P51884 -1.7601864 0.2279993 9.130509 -7.720140 0.0000271 0.0021835 Lumican
P02452 -2.3897612 0.2873949 8.265405 -8.315253 0.0000272 0.0021835 Collagen alpha-1(I) chain
Q16647 -2.1622988 0.2781065 9.001381 -7.775074 0.0000278 0.0021835 Prostacyclin synthase
O43677 -2.8449373 0.3478249 8.403733 -8.179222 0.0000279 0.0021835 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Q15113 -2.3511987 0.3104783 9.158959 -7.572828 0.0000311 0.0023404 Procollagen C-endopeptidase enhancer 1
P18428 -1.8452405 0.2440695 9.111796 -7.560308 0.0000324 0.0023530 Lipopolysaccharide-binding protein
P54652 -2.1599833 0.2893918 9.051681 -7.463873 0.0000372 0.0026082 Heat shock-related 70 kDa protein 2
Q9BW30 -2.5255943 0.3418532 8.972354 -7.387951 0.0000422 0.0026687 Tubulin polymerization-promoting protein family member 3
P02775 -2.0838997 0.2897913 9.340284 -7.191038 0.0000423 0.0026687 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)
P00748 -1.9533971 0.2666667 9.076240 -7.325239 0.0000425 0.0026687 Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Coagulation factor XIIa light chain
P51888 -2.4233975 0.2745778 7.132475 -8.825905 0.0000433 0.0026687 Prolargin
P48681 -1.4123446 0.1992043 9.337319 -7.089932 0.0000475 0.0028423 Nestin
P08294 -2.3175953 0.2952549 7.934754 -7.849472 0.0000524 0.0029143 Extracellular superoxide dismutase [Cu-Zn]
O00180 -4.4369891 0.5875768 8.340284 -7.551334 0.0000529 0.0029143 Potassium channel subfamily K member 1
P14854 1.7251878 0.2298114 8.404606 7.506974 0.0000530 0.0029143 Cytochrome c oxidase subunit 6B1
P02743 -1.8823835 0.2740821 9.340284 -6.867955 0.0000611 0.0032712 Serum amyloid P-component;Serum amyloid P-component(1-203)
P01031 -1.4711401 0.2049598 8.464855 -7.177701 0.0000712 0.0037129 Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain
Q5NDL2 -2.5014769 0.3604862 8.637646 -6.939174 0.0000827 0.0042070 EGF domain-specific O-linked N-acetylglucosamine transferase
Q92508 3.5430878 0.4018569 6.340284 8.816790 0.0000867 0.0043010 Piezo-type mechanosensitive ion channel component 1
Q53GQ0 -1.8169289 0.2782870 9.330707 -6.528975 0.0000914 0.0043253 Very-long-chain 3-oxoacyl-CoA reductase
P05997 -2.5486728 0.3801778 8.913310 -6.703898 0.0000922 0.0043253 Collagen alpha-2(V) chain
P23083 -3.2601200 0.4260786 7.340284 -7.651452 0.0000947 0.0043253 Ig heavy chain V-I region V35
P60468 -1.9513827 0.2769657 8.195483 -7.045576 0.0000957 0.0043253 Protein transport protein Sec61 subunit beta
Q9ULL5-3 -2.3006667 0.3177480 7.819264 -7.240539 0.0000996 0.0044056 Proline-rich protein 12
Q8TBP6 -1.7084465 0.2591582 8.951972 -6.592291 0.0001027 0.0044424 Solute carrier family 25 member 40
P28066 -1.6712466 0.2500754 8.702920 -6.682971 0.0001056 0.0044436 Proteasome subunit alpha type-5
P35625 -2.9679404 0.4179011 7.913419 -7.102016 0.0001074 0.0044436 Metalloproteinase inhibitor 3
Q14195-2 -2.2534620 0.3503505 9.203313 -6.432021 0.0001092 0.0044436 Dihydropyrimidinase-related protein 3
P46060 -1.7047689 0.2516033 8.340284 -6.775622 0.0001164 0.0046204 Ran GTPase-activating protein 1
Q15327 -1.7740861 0.2787606 9.209552 -6.364193 0.0001181 0.0046204 Ankyrin repeat domain-containing protein 1
Q69YU5 2.5059630 0.3833819 8.668560 6.536467 0.0001266 0.0047178 Uncharacterized protein C12orf73
Q6PCB0 -1.8163629 0.2824740 8.907178 -6.430196 0.0001266 0.0047178 von Willebrand factor A domain-containing protein 1
Q9ULD0 -2.0406330 0.2794985 7.340284 -7.301052 0.0001289 0.0047178 2-oxoglutarate dehydrogenase-like, mitochondrial
P00325 -1.5034066 0.2354055 8.957138 -6.386455 0.0001300 0.0047178 Alcohol dehydrogenase 1B
Q92604 -2.0782169 0.3336017 9.272310 -6.229636 0.0001351 0.0047178 Acyl-CoA:lysophosphatidylglycerol acyltransferase 1
P30405 -1.6803249 0.2711663 9.340284 -6.196658 0.0001363 0.0047178 Peptidyl-prolyl cis-trans isomerase F, mitochondrial
P07451 -1.2833190 0.2071973 9.340284 -6.193706 0.0001368 0.0047178 Carbonic anhydrase 3
O14980 -1.1146843 0.1807386 9.340284 -6.167384 0.0001414 0.0047930 Exportin-1
P04004 -1.7677440 0.2765287 8.705024 -6.392625 0.0001463 0.0048767 Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B
P36955 -1.6933164 0.2549225 8.116692 -6.642476 0.0001518 0.0049799 Pigment epithelium-derived factor
P41240 -1.3344948 0.2140799 8.970235 -6.233628 0.0001548 0.0049799 Tyrosine-protein kinase CSK
P04083 -1.3421955 0.2205764 9.340284 -6.084945 0.0001567 0.0049799 Annexin A1
P36021 -2.5034435 0.3868771 8.340284 -6.470901 0.0001616 0.0050582 Monocarboxylate transporter 8
Q6YN16 1.5567113 0.2593836 9.340284 6.001580 0.0001740 0.0053627 Hydroxysteroid dehydrogenase-like protein 2
Q8TBQ9 -1.7482778 0.2799462 8.596029 -6.245050 0.0001829 0.0054987 Protein kish-A
Q8WWA0 -4.4529908 0.6869090 8.075941 -6.482650 0.0001838 0.0054987 Intelectin-1
Q9BXN1 -2.2858485 0.3756082 8.932248 -6.085726 0.0001881 0.0055205 Asporin
Q15274 -2.0357040 0.3094684 7.836023 -6.578068 0.0001900 0.0055205 Nicotinate-nucleotide pyrophosphorylase [carboxylating]
P04003 -1.4359842 0.2391001 8.942972 -6.005787 0.0002063 0.0059093 C4b-binding protein alpha chain
Q9Y6X5 -1.4593292 0.2399025 8.625019 -6.083009 0.0002177 0.0060670 Bis(5-adenosyl)-triphosphatase ENPP4
O15230 -1.3744676 0.2257484 8.609473 -6.088492 0.0002179 0.0060670 Laminin subunit alpha-5
Q7L4S7 -2.1135247 0.3063213 7.072977 -6.899698 0.0002207 0.0060670 Protein ARMCX6
P14550 -1.3048277 0.2184815 8.775886 -5.972256 0.0002317 0.0062011 Alcohol dehydrogenase [NADP(+)]
P23434 1.2727864 0.2204764 9.340284 5.772891 0.0002331 0.0062011 Glycine cleavage system H protein, mitochondrial
Q9UBG0 -1.6345146 0.2806266 9.145533 -5.824517 0.0002366 0.0062011 C-type mannose receptor 2
Q07954 -1.2959588 0.2251011 9.340284 -5.757230 0.0002379 0.0062011 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 0.3056329 9.220990 -5.785639 0.0002408 0.0062011 Tubulin beta-6 chain
P49207 -1.3710319 0.2336941 8.944352 -5.866781 0.0002445 0.0062174 60S ribosomal protein L34
P23142 -2.2973847 0.3545406 7.508971 -6.479891 0.0002527 0.0063459 Fibulin-1
P04196 -1.6877176 0.2602358 7.426268 -6.485340 0.0002636 0.0065233 Histidine-rich glycoprotein
Q9NRG4 2.3970480 0.3977624 8.340284 6.026332 0.0002662 0.0065233 N-lysine methyltransferase SMYD2
Q9NZ01 -1.8635396 0.3161782 8.605914 -5.893954 0.0002748 0.0066360 Very-long-chain enoyl-CoA reductase
O95980 -1.9294212 0.3170843 8.119643 -6.084884 0.0002773 0.0066360 Reversion-inducing cysteine-rich protein with Kazal motifs
P04275 -1.1968998 0.2092499 8.915943 -5.719955 0.0002972 0.0069265 von Willebrand factor;von Willebrand antigen 2
P12110 -1.5935296 0.2653188 8.142157 -6.006093 0.0002997 0.0069265 Collagen alpha-2(VI) chain
O75828 -1.4912698 0.2672188 9.340284 -5.580706 0.0002997 0.0069265 Carbonyl reductase [NADPH] 3
Q9BZH6 2.6654497 0.4508999 8.293516 5.911400 0.0003108 0.0071019 WD repeat-containing protein 11
Q5JPH6 3.4079519 0.4463361 5.749214 7.635394 0.0003228 0.0072954 Probable glutamate–tRNA ligase, mitochondrial
P07357 -1.1909118 0.2141297 9.182819 -5.561637 0.0003267 0.0073022 Complement component C8 alpha chain
P24298 1.6449487 0.2864004 8.561120 5.743528 0.0003360 0.0074285 Alanine aminotransferase 1
Q86WV6 -1.1787564 0.2132658 9.195764 -5.527170 0.0003401 0.0074373 Stimulator of interferon genes protein
P62760 -1.8748180 0.3382166 9.079691 -5.543247 0.0003484 0.0075391 Visinin-like protein 1
P30711 -1.7974916 0.3240448 9.010502 -5.547046 0.0003563 0.0076286 Glutathione S-transferase theta-1
Q9UHG2 -2.3658698 0.4226539 8.817237 -5.597653 0.0003611 0.0076504 ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN
P01024 -1.1291448 0.2055755 9.077710 -5.492603 0.0003724 0.0077554 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
Q92681 -1.8052155 0.3041557 7.852261 -5.935169 0.0003737 0.0077554 Regulatory solute carrier protein family 1 member 1
Q9HCB6 -2.0954145 0.3724083 8.614021 -5.626660 0.0003789 0.0077832 Spondin-1
Q9UQ35 -1.2247564 0.2268752 9.321024 -5.398371 0.0003848 0.0077832 Serine/arginine repetitive matrix protein 2
P12814 -1.9016090 0.3285074 8.129780 -5.788634 0.0003865 0.0077832 Alpha-actinin-1
P48163 -1.9351889 0.3207104 7.544947 -6.034070 0.0003920 0.0078164 NADP-dependent malic enzyme
Q53GG5-2 -2.4399434 0.4302180 8.329769 -5.671411 0.0004055 0.0078164 PDZ and LIM domain protein 3
P25940 -1.6429098 0.3027130 9.075544 -5.427286 0.0004060 0.0078164 Collagen alpha-3(V) chain
Q5M9N0 -2.7584485 0.4859247 8.305567 -5.676699 0.0004072 0.0078164 Coiled-coil domain-containing protein 158
P07585 -2.1323372 0.3954224 9.179678 -5.392555 0.0004087 0.0078164 Decorin
Q9Y3B4 -1.2875533 0.2365495 8.988346 -5.443060 0.0004112 0.0078164 Splicing factor 3B subunit 6
P19429 2.2365865 0.3911075 8.131116 5.718597 0.0004190 0.0078505 Troponin I, cardiac muscle
P50453 -1.2078225 0.2217770 8.918514 -5.446113 0.0004208 0.0078505 Serpin B9
P49458 -1.8786710 0.3060840 7.171760 -6.137763 0.0004301 0.0078505 Signal recognition particle 9 kDa protein
Q53T59 -1.8080103 0.3136764 7.957563 -5.763935 0.0004306 0.0078505 HCLS1-binding protein 3
Q9UNW9 3.3060326 0.6141163 9.062101 5.383398 0.0004323 0.0078505 RNA-binding protein Nova-2
O94919 -1.1297756 0.2125263 9.104029 -5.315934 0.0004654 0.0083194 Endonuclease domain-containing 1 protein
P02747 -1.8530999 0.3004098 6.963608 -6.168573 0.0004687 0.0083194 Complement C1q subcomponent subunit C
P01008 -1.5453986 0.2939965 9.296494 -5.256521 0.0004704 0.0083194 Antithrombin-III
O00264 -1.4077482 0.2656832 9.017305 -5.298598 0.0004916 0.0085501 Membrane-associated progesterone receptor component 1
Q00G26 1.4810539 0.2539535 7.523732 5.831989 0.0004918 0.0085501 Perilipin-5
O60760 -2.2693850 0.4130993 8.340284 -5.493558 0.0005003 0.0086244 Hematopoietic prostaglandin D synthase
Q6SZW1 -2.0732831 0.3523105 7.340284 -5.884817 0.0005099 0.0087149 Sterile alpha and TIR motif-containing protein 1
Q9ULC3 -1.4313739 0.2682133 8.640607 -5.336699 0.0005393 0.0091418 Ras-related protein Rab-23
Q9BS26 -1.1794250 0.2293042 9.274757 -5.143496 0.0005532 0.0092800 Endoplasmic reticulum resident protein 44
P14543 -1.3732462 0.2648209 9.073226 -5.185566 0.0005603 0.0092800 Nidogen-1
Q9BTV4 -1.5944595 0.3084751 9.131742 -5.168844 0.0005614 0.0092800 Transmembrane protein 43
Q8WZA9 -1.0848657 0.2104387 9.151176 -5.155257 0.0005680 0.0092800 Immunity-related GTPase family Q protein
P08603 -1.1479994 0.2248612 9.340284 -5.105370 0.0005703 0.0092800 Complement factor H
Q9UKR5 -3.6937409 0.7025277 8.467917 -5.257787 0.0006374 0.0102887 Probable ergosterol biosynthetic protein 28
Q2TAA5 -1.1153927 0.2211508 9.154381 -5.043584 0.0006610 0.0105534 GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
P11586 1.2736427 0.2366795 7.968800 5.381298 0.0006693 0.0105534 C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
P13671 -1.3576211 0.2723803 9.340284 -4.984285 0.0006753 0.0105534 Complement component C6
Q9UJC5 -1.2143605 0.2433707 9.300212 -4.989756 0.0006789 0.0105534 SH3 domain-binding glutamic acid-rich-like protein 2
Q8WY22 -1.5074312 0.2873530 8.340284 -5.245922 0.0006797 0.0105534 BRI3-binding protein
O14967 -1.6233066 0.3144919 8.500434 -5.161681 0.0007117 0.0108884 Calmegin
Q6PI78 1.5422623 0.3069604 9.012099 5.024304 0.0007120 0.0108884 Transmembrane protein 65
P01042 -1.9829048 0.3548676 7.226305 -5.587732 0.0007401 0.0112337 Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl-bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor
Q8WWQ0 -1.3446280 0.2745911 9.340284 -4.896838 0.0007641 0.0114982 PH-interacting protein
Q92621 -1.2226648 0.2501455 9.337319 -4.887815 0.0007746 0.0114982 Nuclear pore complex protein Nup205
Q9HAT2 1.5992357 0.3251396 9.191154 4.918612 0.0007767 0.0114982 Sialate O-acetylesterase
P20774 -1.9551933 0.3726539 7.989984 -5.246673 0.0007801 0.0114982 Mimecan
Q12996 -1.6262833 0.2741811 6.413766 -5.931420 0.0008037 0.0117599 Cleavage stimulation factor subunit 3
Q16082 -1.2629563 0.2562519 8.979301 -4.928574 0.0008205 0.0119026 Heat shock protein beta-2
Q9BUH6 -1.0828646 0.2214788 9.116217 -4.889247 0.0008288 0.0119026 Protein PAXX
Q8TDB4 -2.3381087 0.3884668 6.205964 -6.018812 0.0008377 0.0119026 Protein MGARP
Q14314 -1.9054905 0.3945281 9.337319 -4.829797 0.0008413 0.0119026 Fibroleukin
P02461 -2.9334098 0.5777570 8.336698 -5.077238 0.0008427 0.0119026 Collagen alpha-1(III) chain
P45877 -0.9878277 0.2055025 9.340284 -4.806890 0.0008685 0.0121826 Peptidyl-prolyl cis-trans isomerase C
P02790 -1.3146905 0.2739791 9.326642 -4.798507 0.0008826 0.0122722 Hemopexin
P35052 -1.2972987 0.2488026 7.767251 -5.214168 0.0008881 0.0122722 Glypican-1;Secreted glypican-1
P01034 -1.4676678 0.2986068 8.779058 -4.915051 0.0008930 0.0122722 Cystatin-C
P50479 -2.0822296 0.4116317 8.111951 -5.058477 0.0009383 0.0126725 PDZ and LIM domain protein 4
P40261 -1.4439118 0.3019097 9.193837 -4.782594 0.0009399 0.0126725 Nicotinamide N-methyltransferase
Q86VU5 1.3843626 0.2916026 9.340284 4.747429 0.0009458 0.0126725 Catechol O-methyltransferase domain-containing protein 1
Q86VP6 -1.3506010 0.2728852 8.472882 -4.949338 0.0009470 0.0126725 Cullin-associated NEDD8-dissociated protein 1
P28300 -1.4644405 0.2845368 7.745124 -5.146753 0.0009713 0.0129124 Protein-lysine 6-oxidase
O95183 -1.4512639 0.3075185 9.340284 -4.719273 0.0009850 0.0129176 Vesicle-associated membrane protein 5
Q9HAV4 -1.8358132 0.3541950 7.590421 -5.183058 0.0009910 0.0129176 Exportin-5
P06727 -1.0726685 0.2216090 8.760880 -4.840366 0.0009941 0.0129176 Apolipoprotein A-IV
Q15126 -0.9960340 0.2116015 9.340284 -4.707122 0.0010024 0.0129176 Phosphomevalonate kinase
Q9NRX4 1.4050508 0.2966068 9.191434 4.737082 0.0010034 0.0129176 14 kDa phosphohistidine phosphatase
O43175 -2.0597036 0.4363756 9.141409 -4.720025 0.0010436 0.0133501 D-3-phosphoglycerate dehydrogenase
Q96H79 -2.2370397 0.3848721 6.120849 -5.812423 0.0010614 0.0134930 Zinc finger CCCH-type antiviral protein 1-like
P13667 -1.0953363 0.2337888 9.092143 -4.685153 0.0011128 0.0140125 Protein disulfide-isomerase A4
O43143 -0.8789725 0.1897614 9.340284 -4.631987 0.0011179 0.0140125 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
Q15582 -2.2645249 0.4572890 7.988009 -4.952065 0.0011229 0.0140125 Transforming growth factor-beta-induced protein ig-h3
P34932 -0.8861862 0.1918489 9.211678 -4.619187 0.0011812 0.0146503 Heat shock 70 kDa protein 4
Q09161 1.9700086 0.3470688 6.133648 5.676132 0.0011944 0.0147236 Nuclear cap-binding protein subunit 1
Q9UKX3 1.7720370 0.3848123 9.158347 4.604939 0.0012243 0.0150011 Myosin-13
Q9NY15 -1.4385610 0.3149447 9.323614 -4.567662 0.0012337 0.0150255 Stabilin-1
P46940 -1.1105871 0.2427582 9.159745 -4.574870 0.0012780 0.0154733 Ras GTPase-activating-like protein IQGAP1
P26447 -1.4990741 0.3219301 8.678479 -4.656521 0.0013126 0.0157975 Protein S100-A4
O60262 -1.2559109 0.2698566 8.619942 -4.653994 0.0013411 0.0160005 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7
O95445 -2.5298428 0.5544888 9.021687 -4.562478 0.0013530 0.0160005 Apolipoprotein M
Q96CS3 -1.1510089 0.2521641 9.011412 -4.564523 0.0013530 0.0160005 FAS-associated factor 2
P00747 -0.8238672 0.1831296 9.326044 -4.498820 0.0013640 0.0160368 Plasminogen;Plasmin heavy chain A;Activation peptide;Angiostatin;Plasmin heavy chain A, short form;Plasmin light chain B
P27658 -1.6133702 0.3601904 9.340284 -4.479215 0.0013987 0.0162290 Collagen alpha-1(VIII) chain;Vastatin
Q96JB2 -2.0512914 0.4376591 8.340284 -4.686962 0.0014012 0.0162290 Conserved oligomeric Golgi complex subunit 3
Q6UWS5 1.3529266 0.2696366 7.211958 5.017593 0.0014046 0.0162290 Protein PET117 homolog, mitochondrial
P01019 -1.0239723 0.2261637 9.047245 -4.527571 0.0014123 0.0162290 Angiotensinogen;Angiotensin-1;Angiotensin-2;Angiotensin-3;Angiotensin-4;Angiotensin 1-9;Angiotensin 1-7;Angiotensin 1-5;Angiotensin 1-4
Q9BXV9 1.4430515 0.3216190 9.209234 4.486836 0.0014327 0.0163716 Uncharacterized protein C14orf142
Q07507 -1.2545210 0.2625554 7.848548 -4.778119 0.0014700 0.0166916 Dermatopontin
P09619 -1.2391198 0.2767381 9.146538 -4.477590 0.0014771 0.0166916 Platelet-derived growth factor receptor beta
P02748 -1.2229145 0.2702446 8.832902 -4.525213 0.0015060 0.0169237 Complement component C9;Complement component C9a;Complement component C9b
Q96LL9 -1.2440322 0.2754799 8.730254 -4.515873 0.0015718 0.0175666 DnaJ homolog subfamily C member 30
Q04721 1.1483233 0.2598866 9.133444 4.418556 0.0016158 0.0179596 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain
Q92930 -1.4774889 0.3095117 7.581882 -4.773612 0.0016269 0.0179842 Ras-related protein Rab-8B
Q9UQR1 -1.7724910 0.3623699 7.153724 -4.891386 0.0016640 0.0182143 Zinc finger protein 148
Q99983 -2.9528995 0.5916370 6.869856 -4.991067 0.0016706 0.0182143 Osteomodulin
P03950 -1.7791248 0.3864958 8.125070 -4.603219 0.0016787 0.0182143 Angiogenin
O95486 -1.3819063 0.3129832 8.998127 -4.415273 0.0016835 0.0182143 Protein transport protein Sec24A
P54577 -1.0184999 0.2305927 8.936604 -4.416879 0.0017078 0.0183797 Tyrosine–tRNA ligase, cytoplasmic;Tyrosine–tRNA ligase, cytoplasmic, N-terminally processed
Q9UBV8 -1.1380629 0.2576995 8.877223 -4.416239 0.0017373 0.0185987 Peflin
P83916 -1.6056296 0.3103606 6.340284 -5.173433 0.0017491 0.0186264 Chromobox protein homolog 1
Q7Z3T8 -1.3746348 0.3073227 8.506070 -4.472936 0.0017814 0.0188721 Zinc finger FYVE domain-containing protein 16
P15924 0.9266546 0.2150747 9.303671 4.308524 0.0018203 0.0189022 Desmoplakin
Q9H1E5 -1.0067111 0.2342197 9.340284 -4.298150 0.0018322 0.0189022 Thioredoxin-related transmembrane protein 4
O15061 -1.1041834 0.2569089 9.340284 -4.297956 0.0018327 0.0189022 Synemin
P00352 -1.1346512 0.2507068 8.171275 -4.525809 0.0018337 0.0189022 Retinal dehydrogenase 1
O75489 1.0163873 0.2366781 9.340284 4.294387 0.0018426 0.0189022 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
P62857 -1.3551185 0.2909568 7.633329 -4.657456 0.0018454 0.0189022 40S ribosomal protein S28
P80723 -1.5107829 0.3303528 7.947336 -4.573240 0.0018493 0.0189022 Brain acid soluble protein 1
Q9NS69 -1.0847694 0.2470228 8.715325 -4.391374 0.0018821 0.0190757 Mitochondrial import receptor subunit TOM22 homolog
P19447 -1.5879548 0.3360346 7.340284 -4.725570 0.0018851 0.0190757 TFIIH basal transcription factor complex helicase XPB subunit
Q96CX2 -0.9045513 0.2117869 9.261157 -4.271044 0.0019459 0.0195934 BTB/POZ domain-containing protein KCTD12
Q9NS86 -0.9960486 0.2315739 9.044392 -4.301213 0.0019646 0.0196781 LanC-like protein 2
Q08945 -1.3761500 0.3103717 8.340284 -4.433877 0.0019736 0.0196781 FACT complex subunit SSRP1
Q9Y287 -1.6105936 0.3791382 9.278002 -4.248038 0.0020060 0.0198114 Integral membrane protein 2B;BRI2, membrane form;BRI2 intracellular domain;BRI2C, soluble form;Bri23 peptide
Q9BYN0 -1.2801043 0.2991701 9.091321 -4.278851 0.0020065 0.0198114 Sulfiredoxin-1
P52907 -0.8523732 0.2014498 9.340284 -4.231194 0.0020269 0.0198425 F-actin-capping protein subunit alpha-1
O15118 -2.1247916 0.4225163 6.340284 -5.028898 0.0020291 0.0198425 Niemann-Pick C1 protein
P62328 -1.3455146 0.2911084 7.439296 -4.622040 0.0020642 0.0200585 Thymosin beta-4;Hematopoietic system regulatory peptide
Q8N142 1.0768090 0.2540502 9.199574 4.238567 0.0020740 0.0200585 Adenylosuccinate synthetase isozyme 1
Q9UBB5 1.4388020 0.2874907 6.340284 5.004690 0.0020808 0.0200585 Methyl-CpG-binding domain protein 2
P82663 -1.3399129 0.3181743 9.292843 -4.211254 0.0021128 0.0202707 28S ribosomal protein S25, mitochondrial
Q14118 -0.8487363 0.1976210 8.701665 -4.294768 0.0021684 0.0207070 Dystroglycan;Alpha-dystroglycan;Beta-dystroglycan
P50991 -1.5101244 0.3476609 8.384169 -4.343670 0.0022074 0.0209776 T-complex protein 1 subunit delta
P31323 -0.9232942 0.2198886 9.168787 -4.198918 0.0022174 0.0209776 cAMP-dependent protein kinase type II-beta regulatory subunit
Q8NAT1 -0.8308927 0.1990906 9.280761 -4.173440 0.0022436 0.0211271 Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Q07065 -0.9488623 0.2241653 8.879656 -4.232869 0.0022648 0.0212284 Cytoskeleton-associated protein 4
P61009 -0.8882212 0.2071280 8.515327 -4.288272 0.0023008 0.0214668 Signal peptidase complex subunit 3
A5D6W6 -2.1994339 0.4960319 7.769064 -4.434058 0.0023477 0.0217715 Fat storage-inducing transmembrane protein 1
P07384 -0.8641607 0.2081976 9.221341 -4.150676 0.0023548 0.0217715 Calpain-1 catalytic subunit
Q6IC98 -0.9057366 0.2130325 8.575771 -4.251635 0.0023847 0.0219476 GRAM domain-containing protein 4
Q96AG4 -1.0641384 0.2580622 9.269776 -4.123574 0.0024262 0.0222291 Leucine-rich repeat-containing protein 59
P05455 -0.8562036 0.2067909 9.091089 -4.140432 0.0024659 0.0224921 Lupus La protein
Q12988 -1.0103210 0.2450796 9.175518 -4.122420 0.0024840 0.0225556 Heat shock protein beta-3
Q04760 1.3958984 0.3330669 8.703014 4.191046 0.0025172 0.0227556 Lactoylglutathione lyase
P62277 -1.3005300 0.3184048 9.300807 -4.084517 0.0025570 0.0229882 40S ribosomal protein S13
P50238 -1.7621993 0.4231465 8.780984 -4.164513 0.0025655 0.0229882 Cysteine-rich protein 1
Q8IYI6 -0.9330152 0.2293270 9.329422 -4.068493 0.0026038 0.0232159 Exocyst complex component 8
P61925 1.3913131 0.3143890 7.466361 4.425451 0.0026160 0.0232159 cAMP-dependent protein kinase inhibitor alpha
P13796 -0.8819572 0.2148907 9.049591 -4.104213 0.0026291 0.0232159 Plastin-2
Q9H1K0 -1.6022771 0.3598694 7.340284 -4.452385 0.0026366 0.0232159 Rabenosyn-5
Q96A65 -0.8321129 0.2060197 9.337319 -4.038998 0.0027198 0.0238452 Exocyst complex component 4
P05543 -1.1801143 0.2658605 7.268625 -4.438848 0.0027468 0.0239784 Thyroxine-binding globulin
Q9UK22 -1.3974278 0.2951343 6.332093 -4.734888 0.0027785 0.0241207 F-box only protein 2
P62745 -1.1929691 0.2889825 8.649814 -4.128171 0.0027947 0.0241207 Rho-related GTP-binding protein RhoB
P24311 1.1056319 0.2753650 9.340284 4.015151 0.0028198 0.0241207 Cytochrome c oxidase subunit 7B, mitochondrial
Q9Y490 -0.8597753 0.2124061 9.108490 -4.047791 0.0028239 0.0241207 Talin-1
P58546 -1.2963604 0.3174483 8.868781 -4.083690 0.0028287 0.0241207 Myotrophin
O00625 -1.1028338 0.2748947 9.340284 -4.011841 0.0028342 0.0241207 Pirin
Q96FN9 -1.7766077 0.4260997 8.340284 -4.169465 0.0028512 0.0241321 Probable D-tyrosyl-tRNA(Tyr) deacylase 2
O75348 -1.2891767 0.3218004 9.340284 -4.006138 0.0028593 0.0241321 V-type proton ATPase subunit G 1
P04843 -1.5241453 0.3707326 8.591850 -4.111171 0.0029059 0.0244243 Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1
Q8N5M1 -1.2833584 0.3196453 9.042872 -4.014946 0.0030119 0.0252045 ATP synthase mitochondrial F1 complex assembly factor 2
Q9UL18 -1.3184619 0.3119143 7.833453 -4.227001 0.0030283 0.0252045 Protein argonaute-1
Q9NQZ5 1.3550021 0.3388528 9.071965 3.998792 0.0030665 0.0252045 StAR-related lipid transfer protein 7, mitochondrial
P63316 0.8794535 0.2220592 9.340284 3.960446 0.0030688 0.0252045 Troponin C, slow skeletal and cardiac muscles
Q9Y4W6 0.9189304 0.2311068 9.216500 3.976216 0.0030751 0.0252045 AFG3-like protein 2
Q96GK7 -1.2557512 0.2978607 7.830371 -4.215900 0.0030766 0.0252045 Fumarylacetoacetate hydrolase domain-containing protein 2A
Q6P1N0 -1.6508051 0.3714299 6.902362 -4.444459 0.0030962 0.0252045 Coiled-coil and C2 domain-containing protein 1A
Q15125 -1.5522594 0.3870986 8.951214 -4.009984 0.0030979 0.0252045 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Q96C86 -0.8529077 0.2137957 9.069123 -3.989358 0.0031127 0.0252237 m7GpppX diphosphatase
Q9HB40 -1.4736038 0.3174494 6.281185 -4.642011 0.0031377 0.0252362 Retinoid-inducible serine carboxypeptidase
Q9NNX1 3.4412993 0.7452169 6.340284 4.617850 0.0031442 0.0252362 Tuftelin
Q3ZCW2 -1.3933792 0.3124556 6.803341 -4.459447 0.0031514 0.0252362 Galectin-related protein
Q9UKS6 0.9882506 0.2470034 8.911835 4.000960 0.0031683 0.0252384 Protein kinase C and casein kinase substrate in neurons protein 3
P00492 -0.9642312 0.2412041 8.922801 -3.997574 0.0031765 0.0252384 Hypoxanthine-guanine phosphoribosyltransferase
Q00577 -1.0249972 0.2569977 8.917577 -3.988352 0.0032246 0.0255207 Transcriptional activator protein Pur-alpha
Q53FA7 1.3758827 0.3490509 9.120295 3.941782 0.0033096 0.0260917 Quinone oxidoreductase PIG3
P14555 -3.1616763 0.7182916 6.836488 -4.401662 0.0033351 0.0261917 Phospholipase A2, membrane associated
P25311 -1.0782056 0.2688958 8.476167 -4.009753 0.0034623 0.0270540 Zinc-alpha-2-glycoprotein
P09467 -1.4304382 0.3349155 7.193752 -4.271043 0.0034715 0.0270540 Fructose-1,6-bisphosphatase 1
Q9UHD9 -0.8978150 0.2287693 9.001107 -3.924544 0.0034860 0.0270629 Ubiquilin-2
P50552 -0.9233883 0.2353450 8.956759 -3.923552 0.0035249 0.0272611 Vasodilator-stimulated phosphoprotein
P01303 -1.3886725 0.3536434 8.910350 -3.926760 0.0035435 0.0273010 Pro-neuropeptide Y;Neuropeptide Y;C-flanking peptide of NPY
O95810 -0.7267426 0.1880408 9.311413 -3.864814 0.0035821 0.0274946 Serum deprivation-response protein
Q7L4E1 -1.9056994 0.4908106 9.123853 -3.882760 0.0036204 0.0276489 Protein FAM73B
P53618 -0.9076351 0.2355834 9.340284 -3.852712 0.0036294 0.0276489 Coatomer subunit beta
Q9BVC6 -1.1958920 0.3111615 9.340284 -3.843317 0.0036832 0.0279539 Transmembrane protein 109
Q8IYU8 -3.0629900 0.6865071 6.340284 -4.461702 0.0037367 0.0282542 Calcium uptake protein 2, mitochondrial
O15031 -0.9094327 0.2346316 8.978611 -3.876003 0.0037712 0.0284097 Plexin-B2
Q96MM6 1.8061841 0.4159279 6.664122 4.342541 0.0038012 0.0285302 Heat shock 70 kDa protein 12B
Q92575 -0.9922287 0.2537821 8.675824 -3.909766 0.0038281 0.0286267 UBX domain-containing protein 4
P28070 -0.9263111 0.2295404 7.851859 -4.035504 0.0039076 0.0289259 Proteasome subunit beta type-4
Q7KZF4 -0.8794696 0.2312497 9.340284 -3.803117 0.0039229 0.0289259 Staphylococcal nuclease domain-containing protein 1
P21980 -0.9178411 0.2377886 8.896829 -3.859904 0.0039321 0.0289259 Protein-glutamine gamma-glutamyltransferase 2
A6NDG6 1.0711621 0.2799207 9.090976 3.826663 0.0039738 0.0289259 Phosphoglycolate phosphatase
Q14258 -0.9919848 0.2501681 8.171292 -3.965273 0.0039740 0.0289259 E3 ubiquitin/ISG15 ligase TRIM25
Q8IUX7 -2.3978246 0.5038072 5.477799 -4.759409 0.0039859 0.0289259 Adipocyte enhancer-binding protein 1
P27695 -1.4919668 0.3933717 9.340284 -3.792766 0.0039872 0.0289259 DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial
Q9Y2D4 -1.5165389 0.3902554 8.642469 -3.886017 0.0039952 0.0289259 Exocyst complex component 6B
P14625 -0.9671286 0.2550590 9.323092 -3.791784 0.0040067 0.0289259 Endoplasmin
P43121 -1.0780079 0.2752938 8.431822 -3.915845 0.0040104 0.0289259 Cell surface glycoprotein MUC18
Q9Y5U8 -2.4800568 0.6536705 9.239505 -3.794047 0.0040581 0.0291505 Mitochondrial pyruvate carrier 1
P10109 0.8708452 0.2285373 9.095706 3.810516 0.0040702 0.0291505 Adrenodoxin, mitochondrial
E5RK69 -1.1254137 0.2982486 9.340284 -3.773408 0.0041105 0.0293363 Annexin
Q15738 -1.0818010 0.2875670 9.340284 -3.761910 0.0041857 0.0297519 Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
Q96PK6 -0.9252023 0.2437075 9.038611 -3.796364 0.0042081 0.0297519 RNA-binding protein 14
Q9BWJ5 -1.1786521 0.3136768 9.340284 -3.757537 0.0042146 0.0297519 Splicing factor 3B subunit 5
P62312 -1.5682756 0.4077365 8.654558 -3.846297 0.0042273 0.0297519 U6 snRNA-associated Sm-like protein LSm6
Q01581 -1.5736067 0.3838132 7.236461 -4.099929 0.0042597 0.0298766 Hydroxymethylglutaryl-CoA synthase, cytoplasmic
P04207 -1.4064185 0.3697442 8.893169 -3.803761 0.0042857 0.0299554 Ig kappa chain V-III region CLL
P31949 -0.9710473 0.2592647 9.292252 -3.745390 0.0043354 0.0301991 Protein S100-A11;Protein S100-A11, N-terminally processed
P49773 -0.9406572 0.2519112 9.340284 -3.734082 0.0043736 0.0302415 Histidine triad nucleotide-binding protein 1
P27169 -1.0408608 0.2742976 8.858327 -3.794641 0.0043768 0.0302415 Serum paraoxonase/arylesterase 1
P78406 -1.6990379 0.3901958 6.220542 -4.354321 0.0044099 0.0302415 mRNA export factor
Q96EM0 -1.2281296 0.3162093 8.220485 -3.883914 0.0044118 0.0302415 Trans-3-hydroxy-L-proline dehydratase
Q13636 -1.9750968 0.4514091 6.153571 -4.375404 0.0044193 0.0302415 Ras-related protein Rab-31
Q9BT09 -1.2017444 0.3192162 9.025143 -3.764672 0.0044307 0.0302415 Protein canopy homolog 3
Q2TAY7 -1.0380001 0.2761436 9.036021 -3.758914 0.0044606 0.0303442 WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed
P01699 -1.9617461 0.4530148 6.221815 -4.330424 0.0045272 0.0306941 Ig lambda chain V-I region VOR
P00488 -1.1450813 0.3076014 9.194665 -3.722614 0.0045771 0.0307988 Coagulation factor XIII A chain
Q04941 -1.3354806 0.3570467 9.042111 -3.740352 0.0045850 0.0307988 Proteolipid protein 2
P01611 -1.3210912 0.3566840 9.340284 -3.703814 0.0045880 0.0307988 Ig kappa chain V-I region Wes
Q9UNN8 -1.2379487 0.3256254 8.426373 -3.801757 0.0047458 0.0317534 Endothelial protein C receptor
P07360 -0.9508577 0.2527506 8.678745 -3.762039 0.0047719 0.0318134 Complement component C8 gamma chain
Q9BXF6 -0.8964783 0.2437972 9.340284 -3.677148 0.0047861 0.0318134 Rab11 family-interacting protein 5
O75165 -0.7578962 0.2054514 9.151616 -3.688932 0.0048643 0.0319713 DnaJ homolog subfamily C member 13
Q9HBL0 1.0363941 0.2729037 8.340284 3.797656 0.0048656 0.0319713 Tensin-1
Q02818 -1.1067621 0.2721030 6.914974 -4.067438 0.0048891 0.0319713 Nucleobindin-1
P20042 -0.8792944 0.2383235 9.117167 -3.689499 0.0048915 0.0319713 Eukaryotic translation initiation factor 2 subunit 2
Q96KP1 -1.0392328 0.2596503 7.187873 -4.002432 0.0049003 0.0319713 Exocyst complex component 2
Q5JUQ0 2.8054144 0.6846327 6.783979 4.097693 0.0049041 0.0319713 Protein FAM78A
P46063 -0.7705141 0.2090192 9.103089 -3.686332 0.0049287 0.0320289 ATP-dependent DNA helicase Q1
Q8IVD9 -0.9380220 0.2458366 8.118654 -3.815632 0.0049828 0.0321151 NudC domain-containing protein 3
Q13011 0.8580498 0.2305395 8.758501 3.721920 0.0049888 0.0321151 Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
P10643 -1.1503065 0.3124712 9.079660 -3.681320 0.0049894 0.0321151 Complement component C7
P31689 -1.4848105 0.3891376 8.075186 -3.815644 0.0050328 0.0321576 DnaJ homolog subfamily A member 1
Q9BU61 -1.2937160 0.3550354 9.340284 -3.643907 0.0050456 0.0321576 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3
Q9BXR6 -1.3408193 0.3679583 9.337319 -3.643944 0.0050480 0.0321576 Complement factor H-related protein 5
Q04837 -1.2706968 0.3399443 8.571099 -3.737955 0.0050592 0.0321576 Single-stranded DNA-binding protein, mitochondrial
Q53GG5 1.0396066 0.2811764 8.835151 3.697347 0.0051012 0.0322937 PDZ and LIM domain protein 3
Q08357 -1.2512681 0.3330234 8.385380 -3.757298 0.0051124 0.0322937 Sodium-dependent phosphate transporter 2
Q9Y5U9 -0.9688010 0.2545575 8.033862 -3.805824 0.0051529 0.0324486 Immediate early response 3-interacting protein 1
Q8NDY3 1.2548368 0.3425443 8.986047 3.663283 0.0052226 0.0326932 [Protein ADP-ribosylarginine] hydrolase-like protein 1
Q9HCN8 -0.8376149 0.2305729 9.245009 -3.632756 0.0052238 0.0326932 Stromal cell-derived factor 2-like protein 1
O75663 -1.6975991 0.4636906 8.909476 -3.661060 0.0053171 0.0330463 TIP41-like protein
P00918 -0.9493414 0.2621743 9.247316 -3.621032 0.0053195 0.0330463 Carbonic anhydrase 2
Q8TDB6 -0.9819803 0.2693888 9.021971 -3.645216 0.0053354 0.0330463 E3 ubiquitin-protein ligase DTX3L
Q9UBI9 -1.9350473 0.4907548 7.151144 -3.943002 0.0053486 0.0330463 Headcase protein homolog
Q9Y5J7 -1.4394711 0.3992113 9.340284 -3.605787 0.0053615 0.0330463 Mitochondrial import inner membrane translocase subunit Tim9
P61020 -0.8349426 0.2277740 8.786883 -3.665663 0.0054054 0.0332161 Ras-related protein Rab-5B
O00299 -0.9153236 0.2535659 9.224749 -3.609806 0.0054367 0.0332504 Chloride intracellular channel protein 1
O15121 -1.3734454 0.3796567 9.148688 -3.617598 0.0054436 0.0332504 Sphingolipid delta(4)-desaturase DES1
Q8NBF2 -0.8115466 0.2254475 9.267369 -3.599715 0.0054830 0.0333221 NHL repeat-containing protein 2
P31994-2 -0.7713913 0.2128135 9.042192 -3.624730 0.0054882 0.0333221 Low affinity immunoglobulin gamma Fc region receptor II-b
Q8WUM0 -0.7928646 0.2207413 9.197018 -3.591827 0.0056211 0.0340275 Nuclear pore complex protein Nup133
Q15493 -1.5865116 0.4393312 8.925679 -3.611197 0.0057264 0.0345622 Regucalcin
P46777 -1.0578875 0.2907731 8.677133 -3.638189 0.0057580 0.0346501 60S ribosomal protein L5
O00567 -1.6066654 0.4506774 9.265594 -3.565001 0.0057960 0.0347761 Nucleolar protein 56
P00742 -1.3361965 0.3282517 6.339061 -4.070646 0.0058516 0.0349072 Coagulation factor X;Factor X light chain;Factor X heavy chain;Activated factor Xa heavy chain
P49756 -0.8733625 0.2459486 9.340284 -3.550996 0.0058522 0.0349072 RNA-binding protein 25
Q9H4A6 -0.9863755 0.2780293 9.253079 -3.547739 0.0059704 0.0355079 Golgi phosphoprotein 3
Q6P1L8 0.6856534 0.1927029 9.122681 3.558085 0.0060067 0.0356199 39S ribosomal protein L14, mitochondrial
O15144 -1.0266458 0.2855485 8.771227 -3.595346 0.0060390 0.0357073 Actin-related protein 2/3 complex subunit 2
Q6PCE3 -1.3068366 0.3419377 7.280703 -3.821855 0.0060595 0.0357246 Glucose 1,6-bisphosphate synthase
P24752 0.8145171 0.2276935 8.835724 3.577253 0.0061362 0.0360726 Acetyl-CoA acetyltransferase, mitochondrial
Q1KMD3 -0.9588418 0.2700047 8.985347 -3.551204 0.0062203 0.0363870 Heterogeneous nuclear ribonucleoprotein U-like protein 2
P06396 -1.1557324 0.3187450 8.375012 -3.625884 0.0062255 0.0363870 Gelsolin
Q96PE7 -1.1472298 0.3269381 9.340284 -3.509012 0.0062598 0.0364828 Methylmalonyl-CoA epimerase, mitochondrial
Q9Y646 -0.6906706 0.1964637 9.214169 -3.515512 0.0063264 0.0367653 Carboxypeptidase Q
Q9HAN9 1.2305740 0.3243878 7.241082 3.793528 0.0063576 0.0367838 Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
P56199 -0.8817502 0.2458511 8.563613 -3.586521 0.0063657 0.0367838 Integrin alpha-1
P62330 -0.7931556 0.2248786 9.042700 -3.527039 0.0063962 0.0368554 ADP-ribosylation factor 6
Q9UBS4 -1.7470606 0.4950790 8.964709 -3.528852 0.0064652 0.0371477 DnaJ homolog subfamily B member 11
P17050 -0.9454418 0.2691014 9.076133 -3.513330 0.0064985 0.0372339 Alpha-N-acetylgalactosaminidase
P01597 -2.2333895 0.6353887 8.962898 -3.514997 0.0066092 0.0377615 Ig kappa chain V-I region DEE
P62191 -1.0000517 0.2865342 9.121769 -3.490166 0.0066894 0.0380720 26S protease regulatory subunit 4
Q9Y5Z7 -1.9019574 0.4706309 6.036385 -4.041293 0.0067078 0.0380720 Host cell factor 2
Q8TCJ2 -0.8698436 0.2472508 8.841000 -3.518061 0.0067197 0.0380720 Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit STT3B
P05062 -2.0647894 0.5535237 7.337319 -3.730264 0.0067568 0.0381759 Fructose-bisphosphate aldolase B
Q9H9B4 -0.7776690 0.2202490 8.678641 -3.530863 0.0067829 0.0382174 Sideroflexin-1
P08754 -1.0292580 0.2989109 9.340284 -3.443361 0.0069577 0.0387675 Guanine nucleotide-binding protein G(k) subunit alpha
P23284 -0.7744408 0.2220342 8.902383 -3.487934 0.0069679 0.0387675 Peptidyl-prolyl cis-trans isomerase B
P60903 -0.8289441 0.2393127 9.121616 -3.463854 0.0069750 0.0387675 Protein S100-A10
P30050 -1.1309945 0.3269340 9.160537 -3.459396 0.0069799 0.0387675 60S ribosomal protein L12
Q68DH5 -0.9839434 0.2762040 8.264512 -3.562380 0.0069946 0.0387675 LMBR1 domain-containing protein 2
O43920 0.8295850 0.2393540 9.084393 3.465933 0.0069949 0.0387675 NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
Q9HAV7 0.8532336 0.2466811 9.084469 3.458853 0.0070738 0.0389187 GrpE protein homolog 1, mitochondrial
P15848 0.9204565 0.2611634 8.490540 3.524446 0.0070912 0.0389187 Arylsulfatase B
Q9GZY4 -1.6172207 0.4452184 7.695874 -3.632421 0.0071156 0.0389187 Cytochrome c oxidase assembly factor 1 homolog
O14807 -0.9860449 0.2855357 9.098006 -3.453315 0.0071204 0.0389187 Ras-related protein M-Ras
Q14019 -2.3417241 0.5998750 6.340284 -3.903687 0.0071323 0.0389187 Coactosin-like protein
P27797 -0.8755252 0.2554349 9.337319 -3.427587 0.0071404 0.0389187 Calreticulin
O75643 -0.7286175 0.2126769 9.340284 -3.425936 0.0071561 0.0389187 U5 small nuclear ribonucleoprotein 200 kDa helicase
Q9Y623 -1.9955095 0.5643610 8.319296 -3.535874 0.0071997 0.0390510 Myosin-4
O75190-3 1.2231318 0.3578584 9.340284 3.417921 0.0072494 0.0392163 DnaJ homolog subfamily B member 6
O43290 -0.7436611 0.2177084 9.340284 -3.415858 0.0072736 0.0392243 U4/U6.U5 tri-snRNP-associated protein 1
Q12907 -1.6602075 0.4691859 8.233905 -3.538485 0.0072911 0.0392243 Vesicular integral-membrane protein VIP36
P17540 0.9216483 0.2495179 7.218599 3.693716 0.0073088 0.0392243 Creatine kinase S-type, mitochondrial
P98160 -0.6944147 0.2027050 9.165822 -3.425740 0.0073588 0.0393888 Basement membrane-specific heparan sulfate proteoglycan core protein;Endorepellin;LG3 peptide
Q16204 -0.7607082 0.2195802 8.775857 -3.464375 0.0073881 0.0394422 Coiled-coil domain-containing protein 6
P21281 -1.3428216 0.3943640 9.297559 -3.405031 0.0074512 0.0396748 V-type proton ATPase subunit B, brain isoform
P30101 -0.7361350 0.2166339 9.321803 -3.398060 0.0075074 0.0398694 Protein disulfide-isomerase A3
P41208 -1.1048997 0.3237758 9.041731 -3.412546 0.0076665 0.0406083 Centrin-2
O75533 -0.7480960 0.2204589 9.201146 -3.393358 0.0077073 0.0407187 Splicing factor 3B subunit 1
Q6ZVF9 -1.5316163 0.3730288 5.430785 -4.105893 0.0078095 0.0411516 G protein-regulated inducer of neurite outgrowth 3
O43707 -1.3709413 0.3968028 8.474549 -3.454969 0.0079041 0.0414605 Alpha-actinin-4
P56192 -1.0251690 0.2995751 8.750500 -3.422077 0.0079248 0.0414605 Methionine–tRNA ligase, cytoplasmic
P32119 -0.8759792 0.2475879 7.817019 -3.538053 0.0079322 0.0414605 Peroxiredoxin-2
P55735 -0.9148870 0.2668382 8.665352 -3.428620 0.0079594 0.0414605 Protein SEC13 homolog
Q92805 1.3677629 0.4006432 8.778556 3.413918 0.0079884 0.0414605 Golgin subfamily A member 1
Q8NBJ5 -1.0090957 0.2942305 8.633867 -3.429609 0.0079904 0.0414605 Procollagen galactosyltransferase 1
P02749 -0.9821379 0.2891685 8.916450 -3.396421 0.0080258 0.0415381 Beta-2-glycoprotein 1
Q5VUM1 0.7587056 0.2250892 9.133835 3.370689 0.0080767 0.0416111 Succinate dehydrogenase assembly factor 4, mitochondrial
Q9UK41 -1.5562781 0.4624749 9.188510 -3.365108 0.0080808 0.0416111 Vacuolar protein sorting-associated protein 28 homolog
Q96G03 -0.8738839 0.2611020 9.340284 -3.346906 0.0081332 0.0417749 Phosphoglucomutase-2
P11021 -0.6930674 0.2052707 8.936719 -3.376359 0.0082570 0.0422676 78 kDa glucose-regulated protein
P43686 -1.2985795 0.3889576 9.318027 -3.338614 0.0082706 0.0422676 26S protease regulatory subunit 6B
Q9BVG4 -1.4282890 0.4286566 9.339601 -3.332012 0.0083331 0.0424471 Protein PBDC1
Q6Y288 -1.0690665 0.3195177 9.178312 -3.345876 0.0083475 0.0424471 Beta-1,3-glucosyltransferase
Q6ICB0 -2.0382992 0.5501145 6.615338 -3.705227 0.0084121 0.0426689 Desumoylating isopeptidase 1
Q9UBQ0 -1.1043560 0.3305598 9.159589 -3.340866 0.0084390 0.0426986 Vacuolar protein sorting-associated protein 29
P61026 -0.8659400 0.2451022 7.522106 -3.532976 0.0085029 0.0429152 Ras-related protein Rab-10
O60568 -1.0635431 0.3214414 9.340284 -3.308669 0.0086546 0.0435732 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Q5T447 -1.0258262 0.3055179 8.790133 -3.357663 0.0087064 0.0437256 E3 ubiquitin-protein ligase HECTD3
Q14011 -1.6060873 0.4696449 8.207070 -3.419790 0.0087487 0.0438299 Cold-inducible RNA-binding protein
P17174 0.8269867 0.2492945 9.111803 3.317309 0.0088277 0.0441170 Aspartate aminotransferase, cytoplasmic
Q9HCJ6 -0.8677868 0.2641736 9.337319 -3.284911 0.0089998 0.0446863 Synaptic vesicle membrane protein VAT-1 homolog-like
Q9BX97 -1.3847012 0.3991892 7.678002 -3.468784 0.0090152 0.0446863 Plasmalemma vesicle-associated protein
P51692 -1.6950637 0.5117158 9.019954 -3.312510 0.0090202 0.0446863 Signal transducer and activator of transcription 5B
Q9BSH5 -0.8065712 0.2426830 8.898230 -3.323559 0.0090307 0.0446863 Haloacid dehalogenase-like hydrolase domain-containing protein 3
Q96LD4 -2.0603233 0.5357700 5.807959 -3.845537 0.0090515 0.0446863 Tripartite motif-containing protein 47
P29992 -1.0018710 0.2970181 8.356168 -3.373097 0.0091420 0.0450239 Guanine nucleotide-binding protein subunit alpha-11
A4D2B0 -1.7140517 0.5077962 8.287008 -3.375472 0.0092198 0.0451888 Metallo-beta-lactamase domain-containing protein 1
P16455 -0.7988054 0.2365251 8.271552 -3.377255 0.0092199 0.0451888 Methylated-DNA–protein-cysteine methyltransferase
P05387 -0.7447264 0.2271759 9.181481 -3.278193 0.0093050 0.0454961 60S acidic ribosomal protein P2
P16083 -1.0028849 0.2987829 8.328193 -3.356567 0.0094201 0.0459485 Ribosyldihydronicotinamide dehydrogenase [quinone]
I3L505 1.1922390 0.3592663 8.662083 3.318538 0.0094484 0.0459760 Acyl carrier protein
Q13425 -0.7615654 0.2337365 9.227425 -3.258222 0.0095473 0.0463464 Beta-2-syntrophin
O60927 -0.9472893 0.2681547 6.992473 -3.532622 0.0095809 0.0463991 Protein phosphatase 1 regulatory subunit 11
Q96CN7 -1.0144660 0.3113216 9.111585 -3.258579 0.0097018 0.0468730 Isochorismatase domain-containing protein 1
Q8N392 2.3552996 0.6403814 6.191965 3.677964 0.0097921 0.0471760 Rho GTPase-activating protein 18
P01621 -1.1890923 0.3636283 8.910972 -3.270076 0.0098109 0.0471760 Ig kappa chain V-III region NG9
Q9NX08 -0.7274661 0.2230879 8.918366 -3.260894 0.0099442 0.0475756 COMM domain-containing protein 8
O43592 -0.8026366 0.2484469 9.247272 -3.230616 0.0099570 0.0475756 Exportin-T
Q9UMR3 -1.6328959 0.4736502 7.340284 -3.447473 0.0099642 0.0475756 T-box transcription factor TBX20
Q13825 1.3948092 0.4347406 9.340284 3.208371 0.0101936 0.0485175 Methylglutaconyl-CoA hydratase, mitochondrial
P35754 0.8371729 0.2598873 9.176489 3.221292 0.0102092 0.0485175 Glutaredoxin-1
O95159 -1.7663091 0.5291718 7.981071 -3.337874 0.0102984 0.0488274 Zinc finger protein-like 1
O60503 1.2572380 0.3448864 6.127202 3.645368 0.0103776 0.0490883 Adenylate cyclase type 9
Q6UXG3 1.6474617 0.5135332 9.185933 3.208092 0.0104163 0.0491571 CMRF35-like molecule 9
Q6B0K9 -1.3448839 0.4015784 7.774174 -3.348995 0.0105220 0.0495411 Hemoglobin subunit mu
P34947 -1.4080509 0.4413496 9.281493 -3.190330 0.0105825 0.0495537 G protein-coupled receptor kinase 5
P03915 -1.1507202 0.3509137 8.337301 -3.279211 0.0105831 0.0495537 NADH-ubiquinone oxidoreductase chain 5
Q13541 0.9175109 0.2881063 9.340284 3.184627 0.0105978 0.0495537 Eukaryotic translation initiation factor 4E-binding protein 1

4.6 Interaction

4.6.1 Volcano-plot

volcanoInt <- ggplot(rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV",
                 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"]])$"compartmentRV - compartmentRA - compartmentLV" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
hlp <- order((rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV")[,"adjPval"])[1:25]
heatmap(assay(pe[["proteinRobust"]])[hlp, ])

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

rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval)

4.7 Fold Change LA vs average of other compartment

4.7.1 Volcano-plot

volcanoNew <- ggplot(rowData(pe[["proteinRobust"]])$"-1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA",
                 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()
volcanoNew

4.7.2 Heatmap

sigNamesNew <- rowData(pe[["proteinRobust"]])$"-1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesNew, ])

There are 47 proteins significantly differentially expressed at the 5% FDR level.

rowData(pe[["proteinRobust"]])$"-1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval)

5 Why are there differences in the results?

5.1 Results Old Incoding

oldEncoding <- pe <- msqrob(
  object = pe,
  i = "proteinRobust",
  formula = ~ location*tissue + patient, modelColumnName = "msqrobModelsMainInt")
designMainInt <- model.matrix(~location*tissue + patient, data = colData(pe))
LMainInt <- makeContrast(
  c(
    "tissueV = 0",
    "tissueV + locationR:tissueV = 0",
    "tissueV + 0.5*locationR:tissueV = 0","locationR:tissueV = 0",
     "- 2/3*locationR - 2/3*tissueV - 1/3*locationR:tissueV = 0"
    ),
  parameterNames = colnames(designMainInt)
  )
pe <- hypothesisTest(object = pe, i = "proteinRobust", contrast = LMainInt, overwrite=TRUE,  modelColumn = "msqrobModelsMainInt")

5.2 Compare models

5.2.1 Number of significant proteins?

nSigMainInt <- sapply(colnames(LMainInt), function(x) rowData(pe[["proteinRobust"]])[[x]] %>%  dplyr::filter(adjPval<0.05) %>% nrow)
nSigNew <- sapply(colnames(L), function(x) rowData(pe[["proteinRobust"]])[[x]] %>%  dplyr::filter(adjPval<0.05) %>% nrow)
nSigMainInt
##                                                    tissueV 
##                                                        205 
##                                tissueV + locationR:tissueV 
##                                                         87 
##                          tissueV + 0.5 * locationR:tissueV 
##                                                        445 
##                                          locationR:tissueV 
##                                                          0 
## -2/3 * locationR - 2/3 * tissueV - 1/3 * locationR:tissueV 
##                                                         49
nSigNew
##                                                    compartmentLV 
##                                                              195 
##                                    compartmentRV - compartmentRA 
##                                                               78 
##  1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA 
##                                                              435 
##                    compartmentRV - compartmentRA - compartmentLV 
##                                                                0 
## -1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA 
##                                                               47

5.2.2 Model fit individual protein?

(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getModel
## $coefficients
##   (Intercept) compartmentLV compartmentRA compartmentRV      patient4 
##     0.1572979    -2.2762344     0.9564933    -2.1143544    -0.1633376 
##      patient8 
##    -0.2352707 
## 
## $vcovUnscaled
##               (Intercept) compartmentLV compartmentRA compartmentRV
## (Intercept)     0.5000000 -3.333333e-01 -3.333333e-01 -3.333333e-01
## compartmentLV  -0.3333333  6.666667e-01  3.333333e-01  3.333333e-01
## compartmentRA  -0.3333333  3.333333e-01  6.666667e-01  3.333333e-01
## compartmentRV  -0.3333333  3.333333e-01  3.333333e-01  6.666667e-01
## patient4       -0.2500000  3.094568e-17  7.948114e-17  7.889935e-17
## patient8       -0.2500000  7.117280e-17  5.483073e-17  1.070630e-16
##                    patient4      patient8
## (Intercept)   -2.500000e-01 -2.500000e-01
## compartmentLV  3.094568e-17  7.117280e-17
## compartmentRA  7.948114e-17  5.483073e-17
## compartmentRV  7.889935e-17  1.070630e-16
## patient4       5.000000e-01  2.500000e-01
## patient8       2.500000e-01  5.000000e-01
## 
## $sigma
## [1] 0.6158563
## 
## $df.residual
## [1] 6
## 
## $w
##  [1] 1 1 1 1 1 1 1 1 1 1 1 1
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getModel
## $coefficients
##       (Intercept)         locationR           tissueV          patient4 
##         0.1572979         0.9564933        -2.2762344        -0.1633376 
##          patient8 locationR:tissueV 
##        -0.2352707        -0.7946133 
## 
## $vcovUnscaled
##                   (Intercept)     locationR       tissueV      patient4
## (Intercept)         0.5000000 -3.333333e-01 -3.333333e-01 -2.500000e-01
## locationR          -0.3333333  6.666667e-01  3.333333e-01  1.165256e-16
## tissueV            -0.3333333  3.333333e-01  6.666667e-01  8.220042e-17
## patient4           -0.2500000  1.165256e-16  8.220042e-17  5.000000e-01
## patient8           -0.2500000  1.742095e-16  1.698440e-16  2.500000e-01
## locationR:tissueV   0.3333333 -6.666667e-01 -6.666667e-01  3.962632e-17
##                        patient8 locationR:tissueV
## (Intercept)       -2.500000e-01      3.333333e-01
## locationR          1.742095e-16     -6.666667e-01
## tissueV            1.698440e-16     -6.666667e-01
## patient4           2.500000e-01      3.962632e-17
## patient8           5.000000e-01     -1.677103e-16
## locationR:tissueV -1.677103e-16      1.333333e+00
## 
## $sigma
## [1] 0.6158563
## 
## $df.residual
## [1] 6
## 
## $w
##  [1] 1 1 1 1 1 1 1 1 1 1 1 1

Model fit is equal!

5.2.3 Main effect - Interaction encoding

\[ \begin{array}{ccl} y_i &=& \beta_0 + \beta_Rx_{R,i} + \beta_Vx_{V,i} + \beta_{R:V}x_{R,i}x_{V,i} +\beta_{p4}x_{p4,i} + \beta_{p8}x_{p8,i} + \epsilon_i\\ \epsilon_i&\sim& N(0, \sigma^2) \end{array} \]

Means for patient “.”?

\[ \begin{array}{ccl} \mu^{LA}_. &=& \beta_0 + \beta_{p.}\\ \mu^{RA}_. &=& \beta_0 + \beta_{R}+ \beta_{p.}\\ \mu^{LV}_. &=& \beta_0 + \beta_{L}+ \beta_{p.}\\ \mu^{RV}_. &=& \beta_0 + \beta_{R} + \beta_{L} + \beta_{R:V}+ \beta_{p.} \end{array} \]

5.2.4 Compartment encoding

\[ \begin{array}{ccl} y_i &=& \beta_0 + \beta_{RA}x_{RA,i} + \beta_{LV}x_{LV,i} + \beta_{RV}x_{VR,i} +\beta_{p4}x_{p4,i} + \beta_{p8}x_{p8,i} + \epsilon_i\\ \epsilon_i&\sim& N(0, \sigma^2) \end{array} \] Means for patient “.”?

\[ \begin{array}{ccc} \mu^{LA}_. &=& \beta_0 + \beta_{p.}\\ \mu^{RA}_. &=& \beta_0 + \beta_{RA}+ \beta_{p.}\\ \mu^{LV}_. &=& \beta_0 + \beta_{LV}+ \beta_{p.}\\ \mu^{RV}_. &=& \beta_0 + \beta_{RV}+ \beta_{p.} \end{array} \]

5.2.5 Parameterisation coincides

\[ \begin{array}{ccl} \hat\beta_0^\text{new} &=& \hat\beta_0^\text{mainInt}\\ \hat\beta_{p4}^\text{new} &=& \hat\beta_{p4}^\text{mainInt}\\ \hat\beta_{p8}^\text{new} &=& \hat\beta_{p8}^\text{mainInt}\\ \hat\beta_{LV}^\text{new} &=& \hat\beta_V^\text{mainInt}\\ \hat\beta_{RA}^\text{new} &=& \hat\beta_A^\text{mainInt}\\ \hat\beta_{RV}^\text{new} &=& \hat\beta_R^\text{mainInt}+\hat\beta_V^\text{mainInt}+\hat\beta_{R:V}^\text{mainInt}\\ \hat\sigma^\text{new} &=& \hat\sigma^\text{mainInt}\\ \end{array} \]

(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getSigma
## [1] 0.6158563
coefs <- (rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getCoef
coefs
##   (Intercept) compartmentLV compartmentRA compartmentRV      patient4 
##     0.1572979    -2.2762344     0.9564933    -2.1143544    -0.1633376 
##      patient8 
##    -0.2352707
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getSigma
## [1] 0.6158563
coefsMainInt <- (rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getCoef
coefsMainInt
##       (Intercept)         locationR           tissueV          patient4 
##         0.1572979         0.9564933        -2.2762344        -0.1633376 
##          patient8 locationR:tissueV 
##        -0.2352707        -0.7946133
coefsMainInt[c("tissueV","locationR","locationR:tissueV")] %>% sum
## [1] -2.114354

5.2.6 Posterior variance is slightly different

(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getVarPosterior()
## [1] 0.3362187
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getVarPosterior()
## [1] 0.3338691
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getDfPosterior
## [1] 9.340284
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getDfPosterior()
## [1] 9.420359

Why?

modType <- sapply(rowData(pe[["proteinRobust"]])$msqrobModels, function(x) x@type)
modType %>% as.factor %>% summary()
## fitError      rlm 
##     1115     2178
modTypeMainInt <- sapply(rowData(pe[["proteinRobust"]])$msqrobModelsMainInt, function(x) x@type)
modTypeMainInt %>% as.factor %>% summary()
## fitError      rlm 
##     1211     2082
notFittedInOne <- which(modType!=modTypeMainInt)
modType[notFittedInOne] %>% unique()
## [1] "rlm"
modTypeMainInt[notFittedInOne] %>% unique()
## [1] "fitError"

More fit errors when using main / interaction encoding.

Squeezing will differ slightly + slight differences in FDR control

5.2.7 Example

(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[notFittedInOne[2]]] %>% getModel
## $coefficients
## [1] NA
## 
## $vcovUnscaled
## [1] NA
## 
## $sigma
## [1] NA
## 
## $df.residual
## [1] NA
## 
## $w
## [1] NA
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[notFittedInOne[2]]] %>% getModel
## $coefficients
##   (Intercept) compartmentRA compartmentRV      patient4      patient8 
##     -2.272568      2.624693      0.949859     -2.563157     -2.443269 
## 
## $vcovUnscaled
##               (Intercept) compartmentRA compartmentRV   patient4    patient8
## (Intercept)     0.7333333    -0.1333333   -0.46666667 -0.6666667 -0.53333333
## compartmentRA  -0.1333333     0.9333333    0.26666667 -0.3333333 -0.26666667
## compartmentRV  -0.4666667     0.2666667    0.93333333  0.3333333  0.06666667
## patient4       -0.6666667    -0.3333333    0.33333333  1.3333333  0.66666667
## patient8       -0.5333333    -0.2666667    0.06666667  0.6666667  0.93333333
## 
## $sigma
## [1] 0.825508
## 
## $df.residual
## [1] 2
## 
## $w
## [1] 1 1 1 1 1 1 1
y <- assay(pe[["proteinRobust"]])[notFittedInOne[2],]
y
## Intensity.LA3 Intensity.LA4 Intensity.LA8 Intensity.LV3 Intensity.LV4 
##    -2.8538915    -4.5357473    -4.4344907            NA            NA 
## Intensity.LV8 Intensity.RA3 Intensity.RA4 Intensity.RA8 Intensity.RV3 
##            NA            NA    -2.5110091    -1.7911663    -0.7413851 
## Intensity.RV4 Intensity.RV8 
##            NA    -4.3473016
lm(y ~ -1 +design)
## 
## Call:
## lm(formula = y ~ -1 + design)
## 
## Coefficients:
##   design(Intercept)  designcompartmentLV  designcompartmentRA  
##             -2.2726                   NA               2.6247  
## designcompartmentRV       designpatient4       designpatient8  
##              0.9499              -2.5632              -2.4433
lm(y ~ -1 +designMainInt)
## 
## Call:
## lm(formula = y ~ -1 + designMainInt)
## 
## Coefficients:
##       designMainInt(Intercept)          designMainIntlocationR  
##                         -2.273                           2.625  
##           designMainInttissueV           designMainIntpatient4  
##                         -1.675                          -2.563  
##          designMainIntpatient8  designMainIntlocationR:tissueV  
##                         -2.443                              NA
---
title: "Proteomics data analysis: heart _ HW"
author: "Lieven Clement"
date: "statOmics, Ghent University (https://statomics.github.io)"
output:
    html_document:
      code_download: true
      theme: cosmo
      toc: true
      toc_float: true
      highlight: tango
      number_sections: true
---
# 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.


# 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.

```{r, warning=FALSE, message=FALSE}
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
pe[["peptideRaw"]]
```

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.

```{r}
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

colData(pe)$compartment <- paste0(colData(pe)$location,colData(pe)$tissue) %>% as.factor
```


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

```{r}
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`.
```{r}
pe <- zeroIsNA(pe, "peptideRaw") # convert 0 to NA
```


## Data exploration

`r format(mean(is.na(assay(pe[["peptideRaw"]])))*100,digits=2)`% 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.


# Preprocessing

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

## Log transform the data

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


## Filtering

### 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.

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

### 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
```{r}
pe[["peptideLog"]] %>%
  rowData %>%
  names
```

No information on decoys.

```{r}
pe <- filterFeatures(pe,~ Potential.contaminant != "+")
```


### Drop peptides that were only identified in one sample

We keep peptides that were observed at last twice.

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

We keep `r nrow(pe[["peptideLog"]])` peptides after filtering.

## Normalize the data
```{r}
pe <- normalize(pe, 
                i = "peptideLog", 
                name = "peptideNorm", 
                method = "center.median")
```


## Explore normalized data

After  normalisation the density curves for all samples are comparable.

```{r}
limma::plotDensities(assay(pe[["peptideNorm"]]))
```

This is more clearly seen is a boxplot.

```{r,}
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.

```{r}
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.


## 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.

```{r,warning=FALSE}
pe <- aggregateFeatures(pe,
 i = "peptideNorm",
 fcol = "Proteins",
 na.rm = TRUE,
 name = "proteinRobust",
 fun = MsCoreUtils::robustSummary)
```

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

# Data Analysis

## Estimation

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

```{r, warning=FALSE}
pe <- msqrob(
  object = pe,
  i = "proteinRobust",
  formula = ~ compartment + patient)
```

## Inference

Explore Design
```{r}
library(ExploreModelMatrix)
VisualizeDesign(colData(pe),~ compartment + patient)$plotlist
```

$$
\begin{array}{ccl}
y_i &=& \beta_0 + \beta_{RA}x_{RA,i} + \beta_{LV}x_{LV,i}  + \beta_{RV}x_{VR,i} +\beta_{p4}x_{p4,i} + \beta_{p8}x_{p8,i} + \epsilon_i\\
\epsilon_i&\sim& N(0,
\sigma^2)
\end{array}
$$
Means for patient "."? 

$$
\begin{array}{ccc}
\mu^{LA}_. &=& \beta_0 + \beta_{p.}\\
\mu^{RA}_. &=& \beta_0 + \beta_{RA}+ \beta_{p.}\\
\mu^{LV}_. &=& \beta_0 + \beta_{LV}+ \beta_{p.}\\
\mu^{RV}_. &=& \beta_0 + \beta_{RV}+ \beta_{p.}
\end{array}
$$

$\log_2$ FC after correcting for patient? 

$$
\begin{array}{lcc}
\log_2 \text{FC}_{V-A}^L &=& \beta_{LV}\\
\log_2 \text{FC}_{V-A}^R &=& \beta_{RV} - \beta_{RA}\\
\log_2 \text{FC}_{V-R}^{AVG} &=& \frac{1}{2}\beta_{LV} + \frac{1}{2} \beta_{RV} - \frac{1}{2} \beta_{RA}\\
\log_2 \text{FC}_{V-A}^R - \log \text{FC}_{V-A}^L &=& \beta_{RV} - \beta_{RA} - \beta_{LV}\\
\log_2 \text{FC}_{LA-1/3(LV+RA+RV)} &=& - \frac{1}{3}\beta_{LV} - \frac{1}{3}\beta_{RV} - \frac{1}{3}\beta_{RA} 
\end{array}
$$

```{r}
design <- model.matrix(~compartment + patient, data = colData(pe))
L <- makeContrast(
  c(
    "compartmentLV = 0",
    "compartmentRV-compartmentRA = 0",
    "1/2*compartmentLV+1/2*compartmentRV - 1/2 *compartmentRA = 0",
    "compartmentRV-compartmentRA - compartmentLV  = 0",
     "- 1/3*compartmentLV - 1/3*compartmentRV - 1/3*compartmentRA = 0"
    ),
  parameterNames = colnames(design)
  )


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

## Evaluate results contrast $\log_2 FC_{V-A}^L$

### Volcano-plot


```{r,warning=FALSE}
volcanoLeft <- ggplot(rowData(pe[["proteinRobust"]])$"compartmentLV",
                 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
```


### Heatmap

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

```{r}
sigNamesLeft <- rowData(pe[["proteinRobust"]])$"compartmentLV" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesLeft, ])
```

There are `r length(sigNamesLeft)` proteins significantly differentially expressed at the 5% FDR level.

```{r}
rowData(pe[["proteinRobust"]])$"compartmentLV" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval)  %>%
  knitr::kable(.)
```

## Evaluate results contrast $\log_2 FC_{V-A}^R$

### Volcano-plot


```{r,warning=FALSE}
volcanoRight <- ggplot(rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA",
                 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
```


### Heatmap

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

```{r}
sigNamesRight <- rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesRight, ])
```

There are `r length(sigNamesRight)` proteins significantly differentially expressed at the 5% FDR level.

```{r}
rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA"  %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)
```


## Evaluate results average contrast $\log_2 FC_{V-A}$

### Volcano-plot


```{r,warning=FALSE}
volcanoAvg <- ggplot(rowData(pe[["proteinRobust"]])$"1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA",
                 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
```


### Heatmap

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

```{r}
sigNamesAvg <- rowData(pe[["proteinRobust"]])$"1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesAvg, ])
```

There are `r length(sigNamesAvg)` proteins significantly differentially expressed at the 5% FDR level.

```{r}
rowData(pe[["proteinRobust"]])$"1/2 * compartmentLV + 1/2 * compartmentRV - 1/2 * compartmentRA" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval) %>%
  knitr::kable(.)
```



## Interaction

### Volcano-plot


```{r,warning=FALSE}
volcanoInt <- ggplot(rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV",
                 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
```

### Heatmap

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

```{r}
sigNamesInt <- rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
hlp <- order((rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV")[,"adjPval"])[1:25]
heatmap(assay(pe[["proteinRobust"]])[hlp, ])
```

There are `r length(sigNamesInt)` proteins significantly differentially expressed at the 5% FDR level.

```{r}
rowData(pe[["proteinRobust"]])$"compartmentRV - compartmentRA - compartmentLV" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval)
```

## Fold Change LA vs average of other compartment 


### Volcano-plot


```{r,warning=FALSE}
volcanoNew <- ggplot(rowData(pe[["proteinRobust"]])$"-1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA",
                 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()
volcanoNew
```

### Heatmap


```{r}
sigNamesNew <- rowData(pe[["proteinRobust"]])$"-1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA" %>%
 rownames_to_column("proteinRobust") %>%
 dplyr::filter(adjPval<0.05) %>%
 pull(proteinRobust)
heatmap(assay(pe[["proteinRobust"]])[sigNamesNew, ])
```
There are `r length(sigNamesNew)` proteins significantly differentially expressed at the 5% FDR level.

```{r}
rowData(pe[["proteinRobust"]])$"-1/3 * compartmentLV - 1/3 * compartmentRV - 1/3 * compartmentRA" %>%
  cbind(.,rowData(pe[["proteinRobust"]])$Protein.names) %>%
  na.exclude %>%
  dplyr::filter(adjPval<0.05) %>%
  arrange(pval)
```

# Why are there differences in the results? 


## Results Old Incoding 

```{r, warning=FALSE}
oldEncoding <- pe <- msqrob(
  object = pe,
  i = "proteinRobust",
  formula = ~ location*tissue + patient, modelColumnName = "msqrobModelsMainInt")
```

```{r}
designMainInt <- model.matrix(~location*tissue + patient, data = colData(pe))
LMainInt <- makeContrast(
  c(
    "tissueV = 0",
    "tissueV + locationR:tissueV = 0",
    "tissueV + 0.5*locationR:tissueV = 0","locationR:tissueV = 0",
     "- 2/3*locationR - 2/3*tissueV - 1/3*locationR:tissueV = 0"
    ),
  parameterNames = colnames(designMainInt)
  )
pe <- hypothesisTest(object = pe, i = "proteinRobust", contrast = LMainInt, overwrite=TRUE,  modelColumn = "msqrobModelsMainInt")
```

## Compare models 

### Number of significant proteins? 

```{r}
nSigMainInt <- sapply(colnames(LMainInt), function(x) rowData(pe[["proteinRobust"]])[[x]] %>%  dplyr::filter(adjPval<0.05) %>% nrow)
nSigNew <- sapply(colnames(L), function(x) rowData(pe[["proteinRobust"]])[[x]] %>%  dplyr::filter(adjPval<0.05) %>% nrow)
nSigMainInt
nSigNew
```


### Model fit individual protein? 

```{r}
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getModel
```

```{r}
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getModel
```

Model fit is equal!

### Main effect - Interaction encoding 
$$
\begin{array}{ccl}
y_i &=& \beta_0 + \beta_Rx_{R,i} + \beta_Vx_{V,i} + \beta_{R:V}x_{R,i}x_{V,i} +\beta_{p4}x_{p4,i} + \beta_{p8}x_{p8,i} + \epsilon_i\\
\epsilon_i&\sim& N(0,
\sigma^2)
\end{array}
$$

Means for patient "."? 

$$
\begin{array}{ccl}
\mu^{LA}_. &=& \beta_0 + \beta_{p.}\\
\mu^{RA}_. &=& \beta_0 + \beta_{R}+ \beta_{p.}\\
\mu^{LV}_. &=& \beta_0 + \beta_{L}+ \beta_{p.}\\
\mu^{RV}_. &=& \beta_0 + \beta_{R} + \beta_{L} + \beta_{R:V}+ \beta_{p.}
\end{array}
$$

### Compartment encoding 

$$
\begin{array}{ccl}
y_i &=& \beta_0 + \beta_{RA}x_{RA,i} + \beta_{LV}x_{LV,i}  + \beta_{RV}x_{VR,i} +\beta_{p4}x_{p4,i} + \beta_{p8}x_{p8,i} + \epsilon_i\\
\epsilon_i&\sim& N(0,
\sigma^2)
\end{array}
$$
Means for patient "."? 

$$
\begin{array}{ccc}
\mu^{LA}_. &=& \beta_0 + \beta_{p.}\\
\mu^{RA}_. &=& \beta_0 + \beta_{RA}+ \beta_{p.}\\
\mu^{LV}_. &=& \beta_0 + \beta_{LV}+ \beta_{p.}\\
\mu^{RV}_. &=& \beta_0 + \beta_{RV}+ \beta_{p.}
\end{array}
$$

### Parameterisation coincides 

$$
\begin{array}{ccl}
\hat\beta_0^\text{new} &=& \hat\beta_0^\text{mainInt}\\
\hat\beta_{p4}^\text{new} &=& \hat\beta_{p4}^\text{mainInt}\\
\hat\beta_{p8}^\text{new} &=& \hat\beta_{p8}^\text{mainInt}\\
\hat\beta_{LV}^\text{new} &=& \hat\beta_V^\text{mainInt}\\
\hat\beta_{RA}^\text{new} &=& \hat\beta_A^\text{mainInt}\\
\hat\beta_{RV}^\text{new} &=& \hat\beta_R^\text{mainInt}+\hat\beta_V^\text{mainInt}+\hat\beta_{R:V}^\text{mainInt}\\
\hat\sigma^\text{new} &=& \hat\sigma^\text{mainInt}\\
\end{array}
$$

```{r}
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getSigma
coefs <- (rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getCoef
coefs
```

```{r}
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getSigma
coefsMainInt <- (rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getCoef
coefsMainInt
```

```{r}
coefsMainInt[c("tissueV","locationR","locationR:tissueV")] %>% sum
```



### Posterior variance is slightly different

```{r}
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getVarPosterior()
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getVarPosterior()
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[sigNamesLeft[1]]] %>% getDfPosterior
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[sigNamesLeft[1]]] %>% getDfPosterior()
```

Why? 

```{r}
modType <- sapply(rowData(pe[["proteinRobust"]])$msqrobModels, function(x) x@type)
modType %>% as.factor %>% summary()
```

```{r}
modTypeMainInt <- sapply(rowData(pe[["proteinRobust"]])$msqrobModelsMainInt, function(x) x@type)
modTypeMainInt %>% as.factor %>% summary()
```

```{r}
notFittedInOne <- which(modType!=modTypeMainInt)
modType[notFittedInOne] %>% unique()
```

```{r}
modTypeMainInt[notFittedInOne] %>% unique()
```

More fit errors when using main / interaction encoding. 

Squeezing will differ slightly + slight differences in FDR control

### Example 

```{r}
(rowData(pe[["proteinRobust"]])$"msqrobModelsMainInt")[[notFittedInOne[2]]] %>% getModel
(rowData(pe[["proteinRobust"]])$"msqrobModels")[[notFittedInOne[2]]] %>% getModel
```

```{r}
y <- assay(pe[["proteinRobust"]])[notFittedInOne[2],]
y
lm(y ~ -1 +design)
lm(y ~ -1 +designMainInt)
```

