Mercurial > repos > artbio > gsc_mannwhitney_de
changeset 0:1d5dbc87da15 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 70c7abb20f76651e61325e3aa90809f6874f8b85
| author | artbio |
|---|---|
| date | Mon, 24 Jun 2019 07:21:30 -0400 |
| parents | |
| children | 665783b2f224 |
| files | MannWhitney_DE.R mannwhitney_de.xml test-data/filterCells_100.tsv test-data/filtered-0.05.tab test-data/geneMetadata_log.tsv test-data/geneMetadata_nolog.tsv test-data/signature_2columns.tsv |
| diffstat | 7 files changed, 47192 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MannWhitney_DE.R Mon Jun 24 07:21:30 2019 -0400 @@ -0,0 +1,149 @@ +#################### +# Differential # +# analysis # +#################### + +# Perform a differential analysis between 2 +# groups of cells. + +# Example of command +# Rscript MannWhitney_DE.R --input <input.tsv> --sep <tab> --colnames <TRUE> --metadata <signature.tsv> --column_name <rate> --fdr <0.01> --output <diff_analysis.tsv> + +# load packages that are provided in the conda env +options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +warnings() +library(optparse) + +#Arguments +option_list = list( + make_option( + "--input", + default = NA, + type = 'character', + help = "Input file that contains log2(CPM +1) values" + ), + make_option( + "--sep", + default = '\t', + type = 'character', + help = "File separator [default : '%default' ]" + ), + make_option( + "--colnames", + default = TRUE, + type = 'logical', + help = "Consider first line as header ? [default : '%default' ]" + ), + make_option( + "--comparison_factor_file", + default = NA, + type = 'character', + help = " A two column table : cell identifiers and a comparison factor that split cells in two categories (high/low, HOM/HET,...)" + ), + make_option( + "--factor1", + type = 'character', + help = "First factor of rate category in comparison factor file" + ), + make_option( + "--factor2", + type = 'character', + help = "Second factor of rate category in comparison factor file" + ), + make_option( + "--fdr", + default = 0.01, + type = 'numeric', + help = "FDR threshold [default : '%default' ]" + ), + make_option( + "--log", + default=FALSE, + action="store_true", + type = 'logical', + help = "Expression data are log-transformed [default : '%default' ]" + ), + make_option( + "--output", + default = "results.tsv", + type = 'character', + help = "Output name [default : '%default' ]" + ) +) + +opt = parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) + +if (opt$sep == "tab") {opt$sep = "\t"} +if (opt$sep == "comma") {opt$sep = ","} + +#Open files +data.counts <- read.table( + opt$input, + h = opt$colnames, + row.names = 1, + sep = opt$sep, + check.names = F +) + +metadata <- read.table( + opt$comparison_factor_file, + header = TRUE, + stringsAsFactors = F, + sep = "\t", + check.names = FALSE, + row.names = 1 +) + +metadata <- subset(metadata, rownames(metadata) %in% colnames(data.counts)) + +# Create two logical named vectors for each factor level of cell signature +factor1_cells <- setNames(metadata[,1] == opt$factor1, rownames(metadata)) +factor2_cells <- setNames(metadata[,1] == opt$factor2, rownames(metadata)) + +## Mann-Whitney test (Two-sample Wilcoxon test) +MW_test <- data.frame(t(apply(data.counts, 1, function(x) { + do.call("cbind", wilcox.test(x[names(factor1_cells)[factor1_cells]], x[names(factor2_cells)[factor2_cells]]))[, 1:2] +})), stringsAsFactors = F) + +# Benjamini-Hochberg correction and significativity +MW_test$p.adjust <- p.adjust(as.numeric(MW_test$p.value), method = "BH" , n = nrow(MW_test)) +# MW_test$Critical.value <- (rank(MW_test$p.value) / nrow(MW_test)) * opt$fdr +MW_test$Significant <- MW_test$p.adjust < opt$fdr + +## Descriptive Statistics Function +descriptive_stats <- function(InputData) { + SummaryData = data.frame( + mean = rowMeans(InputData), + SD = apply(InputData, 1, sd), + Variance = apply(InputData, 1, var), + Percentage_Detection = apply(InputData, 1, function(x, y = InputData) { + (sum(x != 0) / ncol(y)) * 100 + }), + mean_factor2 = rowMeans(InputData[,factor2_cells]), + mean_factor1 = rowMeans(InputData[, factor1_cells]) + ) + if(opt$log) { + SummaryData$fold_change <- SummaryData$mean_factor1 - SummaryData$mean_factor2 + } else { + SummaryData$fold_change <- SummaryData$mean_factor1 / SummaryData$mean_factor2 + } + return(SummaryData) +} + +gene_stats <- descriptive_stats(data.counts) + +results <- merge(gene_stats, MW_test, by = "row.names") +colnames(results)[1] <- "genes" + +# Save files +write.table( + results, + opt$output, + sep = "\t", + quote = F, + col.names = T, + row.names = F +)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mannwhitney_de.xml Mon Jun 24 07:21:30 2019 -0400 @@ -0,0 +1,118 @@ +<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.0"> + <description>using a Mann-Whitney test</description> + <requirements> + <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/MannWhitney_DE.R + --input '$input' + --sep + #if $sep == 'tab': + 'tab' + #elif $sep == 'comma': + 'comma' + #end if + --colnames '$colnames' + --factor1 '$factor1' + --factor2 '$factor2' + --comparison_factor_file '$comparison_factor_file' + --fdr '$fdr' + $log + --output '$output' +]]></command> + <inputs> + <param name="input" type="data" format="txt" label="Expression data" help="a csv or tsv table file" /> + <param name="sep" type="select" label="Indicate column separator"> + <option value="tab" selected="true">Tabs</option> + <option value="comma">Comma</option> + </param> + <param name="colnames" type="select" label="Firt row contains column names"> + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">No</option> + </param> + <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table" + help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories." /> + <param name="factor1" type="text" label="The first value that the comparison factor can take." help="typical values could be 'HIGH', 'mutant', 't1', etc."/> + <param name="factor2" type="text" label="The second value that the comparison factor can take." help="typical values could be 'LOW', 'wt', 't2', etc."/> + <param name="fdr" type="float" value="0.01" label="FDR threshold" + help="Reject H0 of no differential expression if adjusted p-values (Benjamini-Hochberg correction) is higher than the FDR cut-off."/> + <param name="log" type="boolean" checked="false" label="Expression data are log-transformed" truevalue="--log" falsevalue=""/> + + </inputs> + <outputs> + <data name="output" format="tabular" label="Results of Mann-Whitney differential analysis from ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="filtered-0.05.tab" ftype="txt"/> + <param name="sep" value="tab" /> + <param name="colnames" value="TRUE"/> + <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/> + <param name="factor1" value="HIGH"/> + <param name="factor2" value="LOW"/> + <param name="fdr" value="0.01"/> + <param name="log" value="true"/> + <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/> + </test> + <test> + <param name="input" value="filterCells_100.tsv" ftype="txt"/> + <param name="sep" value="tab" /> + <param name="colnames" value="TRUE"/> + <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/> + <param name="factor1" value="HIGH"/> + <param name="factor2" value="LOW"/> + <param name="fdr" value="0.01"/> + <param name="log" value="false"/> + <output name="output" file="geneMetadata_nolog.tsv" ftype="tabular"/> + </test> + </tests> + <help> + +**What it does** + +The tools takes a table of gene expression values (e.E. log2(CPM+1), etc...) from single cell RNAseq sequencing libraries (columns) and a metadata file that contains at least two columns : + * Cell identifiers + * Column that differentiate cell in two groups. It must be a column with only two categories (factor levels). + +For each gene (rows in expression data file), this script perform a Mann-Whitney test between +the two groups of cells (high/low, mutant/wild type) and then adjust the returned p-values by using the +Benjamini-Hochberg (BH) correction. A False Discovery Rate (FDR) threshold is used to determine if gene +can be considerated as significant (p-adjust below FDR cut-off) or not (p-adjust above the FDR cut-off). + +**Output** + +The tools returns a result table. For each row (genes) : + +==================== ====================================================================================================== + Column Description +-------------------- ------------------------------------------------------------------------------------------------------ + mean mean expression across all cells + SD standard deviation of its expression across all cells + variance variance of expression across all cells +Percentage_detection (number of cells where the gene is detected (expression value superior to 0) / number of cells) * 100 + mean_factor2 mean expression across cells of the second group (of log transformed expression values) + mean_factor1 mean expression across cells of the first group (of log transformed expression values) + fold_change mean_factor1 - mean_factor2 (difference of log) + statistic W statistic of Mann-Whitney test + p.value p-value of Mann-Whitney test + p.adjust p-values adjusted from the BH correction + Significant TRUE/FALSE vector (if p-adjust inferior to FDR cut-off then the value is TRUE) +==================== ====================================================================================================== + + </help> + <citations> + <citation type="bibtex"> + @Manual{, + title = {R: A Language and Environment for Statistical Computing}, + author = {{R Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2014}, + url = {http://www.R-project.org/}, + } + </citation> + </citations> +</tool>
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0.627535687453043 1012 0.0881545487402983 0.320024156433632 FALSE +ATAD3A 11.81 29.4918906847563 869.771616161616 25 8.35897435897436 24.0454545454545 2.8766034578918 1010 0.0973340695341528 0.340833689887846 FALSE +ATAD3B 10.53 34.7253160641854 1205.84757575758 28 9.53846153846154 14.0454545454545 1.4725073313783 1006 0.12099638592315 0.399582185733772 FALSE +ATAD3C 0.11 0.723278171336114 0.523131313131313 5 0.115384615384615 0.0909090909090909 0.787878787878788 902 0.337757436504941 0.799882350686014 FALSE +ATAD5 1.91 9.47841247415953 89.840303030303 8 0.871794871794872 5.59090909090909 6.41310160427807 973 0.0428475965367639 0.21543211864219 FALSE +ATAT1 20.49 44.8029343826153 2007.30292929293 29 19.7564102564103 23.0909090909091 1.16878060291428 985 0.188985691441203 0.542000200981595 FALSE +ATCAY 0.96 9.6 92.16 1 1.23076923076923 0 0 847 0.612193566468421 0.993316154786423 FALSE +ATE1 4.27 20.4148168611611 416.764747474747 11 4.51282051282051 3.40909090909091 0.755423553719008 977 0.0694818046663329 0.268329329263402 FALSE +ATF1 5.41 19.9975225738317 399.900909090909 14 4.80769230769231 7.54545454545455 1.56945454545455 1001 0.0493580772182661 0.237254400574616 FALSE +ATF2 18.55 34.5725339107521 1195.2601010101 39 14.3589743589744 33.4090909090909 2.32670454545455 1116 0.0148095325444158 0.105831546329636 FALSE +ATF3 165.97 329.379258698246 108490.696060606 55 129.846153846154 294.045454545455 2.26456807410599 1152 0.0104170485053223 0.0827978195484257 FALSE +ATF4 75.6 125.243520367081 15685.9393939394 58 73.2435897435897 83.9545454545455 1.14623744888054 901 0.713228290861103 1 FALSE +ATF5 3.71 13.935127476194 194.187777777778 11 3.1025641025641 5.86363636363636 1.88993238166792 892 0.607826295951348 0.993316154786423 FALSE +ATF6 26.36 58.9696926095486 3477.42464646465 35 24.7692307692308 32 1.29192546583851 1012 0.133697920078923 0.430358575419059 FALSE +ATF6B 30.35 63.5661391025445 4040.65404040404 31 28.0897435897436 38.3636363636364 1.36575245840422 993.5 0.170417111932581 0.509051140437243 FALSE +ATF7 43.2 85.8196370361126 7365.0101010101 54 36.1666666666667 68.1363636363636 1.8839547549225 1202.5 0.00258802959877299 0.0359554552105394 FALSE +ATF7IP 55.23 100.347261189745 10069.5728282828 51 49.8717948717949 74.2272727272727 1.48836176676794 1105 0.0289905449974221 0.165743637983593 FALSE +ATF7IP2 0.02 0.14070529413629 0.0197979797979798 2 0.0128205128205128 0.0454545454545455 3.54545454545455 886 0.345367786595472 0.800436942927817 FALSE +ATG10 5.63 20.5532837947486 422.437474747475 13 4.83333333333333 8.45454545454546 1.74921630094044 966.5 0.124104354247076 0.40607316443343 FALSE +ATG12 44.89 74.2006418606015 5505.73525252525 54 40.1025641025641 61.8636363636364 1.54263543362009 1067 0.0678280283995643 0.263628390081476 FALSE +ATG13 41.62 71.0338914700141 5045.81373737374 48 31.0769230769231 79 2.54207920792079 1214 0.00141830195397841 0.0251082424701269 FALSE +ATG14 15.5 48.6935376211321 2371.06060606061 29 13.2307692307692 23.5454545454545 1.77959830866808 1064.5 0.0324259784594397 0.178716309279226 FALSE +ATG16L1 18.4 77.6269244137586 6025.93939393939 13 18.7692307692308 17.0909090909091 0.910581222056632 913 0.437749851371328 0.916301306363014 FALSE +ATG16L2 13.53 54.366592348945 2955.72636363636 14 13.9102564102564 12.1818181818182 0.875743611227482 906 0.512377481520644 0.98846173434941 FALSE +ATG2A 16.05 57.0601977004651 3255.86616161616 21 20.3974358974359 0.636363636363636 0.0311982172447289 714 0.0935421666705951 0.33226498003212 FALSE +ATG2B 12.63 35.9650939078154 1293.48797979798 17 16.0897435897436 0.363636363636364 0.0226005070626585 713 0.0661556035512854 0.259122384141206 FALSE +ATG3 62.14 86.8211932419706 7537.9195959596 55 55.2307692307692 86.6363636363636 1.56862496834642 1067 0.068784759529079 0.266693588962256 FALSE +ATG4A 10.8 44.0002295678125 1936.0202020202 10 10.1282051282051 13.1818181818182 1.30149597238205 991 0.0341884198059943 0.185357755707351 FALSE +ATG4B 51.17 80.5162703928827 6482.8697979798 52 42.025641025641 83.5909090909091 1.98904542681236 1055 0.0829638009690954 0.306513533762185 FALSE +ATG4C 12.25 32.0398662653737 1026.55303030303 27 14.4102564102564 4.59090909090909 0.31858621805241 863.5 0.957550657185008 1 FALSE +ATG4D 16.96 46.2103053791286 2135.39232323232 22 14.9230769230769 24.1818181818182 1.62043111527648 1096.5 0.00629541458911104 0.0624151109332629 FALSE +ATG5 38.86 83.5050376512179 6973.09131313131 38 33.474358974359 57.9545454545455 1.7313115838585 1074.5 0.0394583905464675 0.202874294893257 FALSE +ATG7 24.95 82.3578512138682 6782.81565656566 33 19.5769230769231 44 2.2475442043222 1019 0.110240469596798 0.372724762713289 FALSE +ATG9A 36.18 79.0382058235002 6247.03797979798 36 30.1025641025641 57.7272727272727 1.91768623199628 1098.5 0.0200821480049009 0.129385066054184 FALSE +ATG9B 0.7 5.32290647422377 28.3333333333333 4 0.807692307692308 0.318181818181818 0.393939393939394 863.5 0.902470833144709 1 FALSE +ATHL1 19.53 84.8971397835896 7207.52434343434 18 20.9615384615385 14.4545454545455 0.689574645537948 864.5 0.94058333110358 1 FALSE +ATIC 64.12 106.957867660801 11439.9854545455 41 45.4871794871795 130.181818181818 2.86194527006252 1294.5 4.70583115926121e-05 0.00435928537168458 TRUE +ATL1 9.04 31.1263050921061 968.846868686869 13 10.1794871794872 5 0.491183879093199 861 0.971604288101673 1 FALSE +ATL2 7.59 32.4317761001475 1051.8201010101 19 7.65384615384615 7.36363636363636 0.962083142987666 1039.5 0.0277863551040558 0.161199490087283 FALSE +ATL3 22.58 75.8918928077261 5759.57939393939 28 12.3717948717949 58.7727272727273 4.75054168629298 1310 2.07948977530646e-06 0.0010798559348747 TRUE +ATM 9.17 21.5570912188584 464.708181818182 29 9.64102564102564 7.5 0.777925531914894 882.5 0.803180581869033 1 FALSE +ATMIN 44.45 98.9455900885926 9790.2297979798 31 40.6538461538462 57.9090909090909 1.42444310656231 1097.5 0.0152304826511586 0.107687116064228 FALSE +ATN1 42.37 46.2393105310172 2138.07383838384 89 39.525641025641 52.4545454545455 1.32710170141244 891 0.786640825615551 1 FALSE +ATOH1 0 0 0 0 0 0 NA 858 NaN NA NA +ATOH7 0 0 0 0 0 0 NA 858 NaN NA NA +ATOH8 3.69 16.6501099580802 277.226161616162 6 1.47435897435897 11.5454545454545 7.83083003952569 944.5 0.082120062548072 0.304198926164858 FALSE +ATOX1 85.08 107.983133737252 11660.3571717172 76 67.2692307692308 148.227272727273 2.20349290503664 1193 0.00506479671239285 0.0544346769772679 FALSE +ATP10A 0.22 1.90999497593078 3.64808080808081 3 0.256410256410256 0.0909090909090909 0.354545454545455 875 0.642227504899165 1 FALSE +ATP10B 1.76 9.33779114321709 87.1943434343434 6 0.82051282051282 5.09090909090909 6.20454545454546 992.5 0.00675072246554805 0.0649180586728094 FALSE +ATP10D 10.12 38.2509734477042 1463.13696969697 14 10.9102564102564 7.31818181818182 0.670761670761671 943 0.243828970671638 0.652070884258965 FALSE +ATP11A 29.09 65.5442012937249 4296.04232323232 48 30.5128205128205 24.0454545454545 0.788044308632544 942 0.453533197832472 0.916301306363014 FALSE +ATP11B 2.06 11.0780700649362 122.723636363636 7 2.47435897435897 0.590909090909091 0.238813000471032 831 0.618121508209938 0.999204674613858 FALSE +ATP11C 13.78 49.5811914485175 2458.29454545455 19 11.2948717948718 22.5909090909091 2.00010318852544 1135 0.000776545912238853 0.0183481545775506 FALSE +ATP12A 0.05 0.411329453348431 0.169191919191919 2 0.0641025641025641 0 0 836 0.460699420081267 0.916301306363014 FALSE +ATP13A1 34.18 73.1157073867624 5345.90666666667 39 29.1666666666667 51.9545454545455 1.7812987012987 1098.5 0.0231254638828626 0.14285255193702 FALSE +ATP13A2 19.03 46.2582681662141 2139.82737373737 25 16.0641025641026 29.5454545454545 1.83922223028368 997.5 0.128220335369312 0.416576939376161 FALSE +ATP13A3 30.48 106.35764707302 11311.9490909091 38 26.4358974358974 44.8181818181818 1.69535314346178 1088.5 0.0283037037810743 0.162761734453598 FALSE +ATP13A4 46.6 99.8131587851355 9962.66666666667 42 42.8846153846154 59.7727272727273 1.39380350591113 930 0.507229348087108 0.981853496197775 FALSE +ATP13A5 3.31 24.4988950482641 600.195858585859 10 1.07692307692308 11.2272727272727 10.4253246753247 944 0.171734062587236 0.512123373871091 FALSE +ATP1A1 169.47 199.121680224313 39649.4435353535 75 116.615384615385 356.863636363636 3.06017630127129 1331 7.40906759490753e-05 0.00530904045378676 TRUE +ATP1A1OS 5.32 26.5085768472139 702.704646464646 12 4.20512820512821 9.27272727272727 2.20509977827051 935 0.259385320169943 0.684275927041231 FALSE +ATP1A2 56.37 170.366548086972 29024.7607070707 24 62.5384615384615 34.5 0.551660516605166 746.5 0.217533753170577 0.601363864200881 FALSE +ATP1A3 0.19 1.62490092938094 2.64030303030303 2 0 0.863636363636364 Inf 936 0.00783414581327792 0.0694811569640497 FALSE +ATP1A4 0.98 7.49003378234078 56.1006060606061 4 1.20512820512821 0.181818181818182 0.150870406189555 863 0.912179800152995 1 FALSE +ATP1B1 10.07 39.2791756069757 1542.85363636364 31 12 3.22727272727273 0.268939393939394 836.5 0.831111590474638 1 FALSE +ATP1B2 194.98 219.341069219753 48110.5046464646 74 188.884615384615 216.590909090909 1.14668369708076 849 0.94311344187484 1 FALSE +ATP1B3 106.06 196.539035113212 38627.5923232323 58 91.1410256410256 158.954545454545 1.74405043542756 1225.5 0.00150542580403144 0.0260198152282594 FALSE +ATP1B4 4.08 40.5982235766019 1648.21575757576 3 5.21794871794872 0.0454545454545455 0.00871119052937235 874.5 0.652332847318063 1 FALSE +ATP2A1 0.39 2.78848642916844 7.77565656565657 2 0 1.77272727272727 Inf 936 0.00783414581327792 0.0694811569640497 FALSE +ATP2A2 36.6 80.8541522705788 6537.39393939394 45 36.0512820512821 38.5454545454545 1.06918401655244 957.5 0.36689490202954 0.811663359900245 FALSE +ATP2A3 0 0 0 0 0 0 NA 858 NaN NA NA +ATP2B1 38.69 73.0371007146921 5334.41808080808 41 26.6666666666667 81.3181818181818 3.04943181818182 1209 0.00106888276837272 0.0215814510333579 FALSE +ATP2B2 4.55 31.2411199504367 976.007575757576 6 5.21794871794872 2.18181818181818 0.418137145409873 842.5 0.761715039925753 1 FALSE +ATP2B3 0.11 1.1 1.21 1 0 0.5 Inf 897 0.0630558447149376 0.252399828906917 FALSE +ATP2B4 77.5 109.551104259357 12001.4444444444 60 66.4102564102564 116.818181818182 1.75903825903826 1180 0.00568699179081338 0.0585950723843594 FALSE +ATP2C1 49.38 87.020812557582 7572.62181818182 51 43.4871794871795 70.2727272727273 1.61594125214408 1075.5 0.0545676406632636 0.252399828906917 FALSE +ATP2C2 1.21 8.19989529373899 67.2382828282828 3 1.43589743589744 0.409090909090909 0.284902597402597 874 0.662524871400905 1 FALSE +ATP4A 0.31 2.31680291729266 5.36757575757576 2 0.128205128205128 0.954545454545455 7.44545454545455 886.5 0.336693018711006 0.799577485898251 FALSE +ATP4B 0 0 0 0 0 0 NA 858 NaN NA NA +ATP5A1 302.42 383.941077655297 147410.751111111 75 219.961538461538 594.772727272727 2.70398512136578 1328.5 8.08814276634879e-05 0.00549429419081507 TRUE +ATP5B 336.3 396.205244740142 156978.595959596 89 259.833333333333 607.409090909091 2.33768732870721 1311.5 0.0001619792286935 0.00771809324124714 TRUE +ATP5C1 107.87 148.476958386536 22045.4071717172 56 91.2948717948718 166.636363636364 1.82525436927908 1113 0.02682362004845 0.157396194544458 FALSE +ATP5D 96.26 106.301231974008 11299.9519191919 75 80.1282051282051 153.454545454545 1.91511272727273 1257.5 0.000818574929877789 0.019052249961538 FALSE +ATP5E 142.26 137.834010844401 18998.2145454545 93 107.641025641026 265 2.4618866126727 1381 1.37021513208682e-05 0.00241994093083239 TRUE +ATP5EP2 0.29 0.624338033278432 0.38979797979798 23 0.282051282051282 0.318181818181818 1.12809917355372 941 0.348706734487528 0.800436942927817 FALSE +ATP5F1 157.23 195.702921374065 38299.6334343434 76 129.987179487179 253.818181818182 1.95264012050677 1165 0.0102182098160205 0.0818577740763685 FALSE +ATP5G1 117.42 145.904852073486 21288.2258585859 74 92.3717948717949 206.227272727273 2.23257838622169 1166 0.0098374144892344 0.0801089872426157 FALSE +ATP5G2 136.9 144.425892359502 20858.8383838384 86 121.192307692308 192.590909090909 1.58913476241309 1181.5 0.00711428547689569 0.0666052175577318 FALSE +ATP5G3 157.84 163.277091120734 26659.4084848485 84 135.987179487179 235.318181818182 1.73044387497107 1187 0.00616141408834818 0.0615561882926551 FALSE +ATP5H 96.18 122.324901038756 14963.3814141414 71 73.7692307692308 175.636363636364 2.38088918380889 1220.5 0.00229106582291754 0.0334610163437107 FALSE +ATP5I 63.95 66.1958183243954 4381.88636363636 89 60.2564102564103 77.0454545454545 1.27862669245648 1070 0.0781998805366301 0.29393192993083 FALSE +ATP5J 127.3 134.421656804928 18069.1818181818 88 110.692307692308 186.181818181818 1.68197611978015 1157 0.0129189554834569 0.0959905092964772 FALSE +ATP5J2 139.63 126.436126326316 15986.094040404 97 123.692307692308 196.136363636364 1.58567955676165 1185.5 0.0065062720362656 0.0637211085261754 FALSE +ATP5J2-PTCD1 0.01 0.1 0.01 1 0 0.0454545454545455 Inf 897 0.0630558447149376 0.252399828906917 FALSE +ATP5L 116.13 130.59024164202 17053.8112121212 76 95.5 189.272727272727 1.98191337458353 1260 0.000767699267629318 0.0182127883106212 FALSE +ATP5L2 0.01 0.1 0.01 1 0.0128205128205128 0 0 847 0.612193566468421 0.993316154786423 FALSE +ATP5O 139.22 206.018562466609 42443.6480808081 66 112.141025641026 235.227272727273 2.09760229481277 1199 0.00384457927194943 0.0459775478131598 FALSE +ATP5S 12.57 32.1989569440196 1036.77282828283 25 9.66666666666667 22.8636363636364 2.36520376175549 1134 0.00257069649614147 0.035799782909317 FALSE +ATP5SL 24.07 55.98597497534 3134.42939393939 29 15.525641025641 54.3636363636364 3.50153892350424 1199 0.000406576380793029 0.0126507169161399 FALSE +ATP6AP1 118.88 166.820188686907 27828.9753535354 60 95.6794871794872 201.136363636364 2.10218898079008 1199.5 0.00335846901539123 0.042239328180494 FALSE +ATP6AP1L 1.47 7.69816323363679 59.2617171717172 6 1.02564102564103 3.04545454545455 2.96931818181818 942.5 0.0894917809278303 0.322119632114247 FALSE +ATP6AP2 124.17 205.304408381822 42149.9001010101 65 94.6025641025641 229 2.42065320504133 1301 0.000167346281906293 0.00783676936991234 TRUE +ATP6V0A1 29.64 73.3342313994597 5377.90949494949 32 23 53.1818181818182 2.31225296442688 1116.5 0.00952132587650809 0.0786476999230262 FALSE +ATP6V0A2 17.67 44.6046731709455 1989.57686868687 23 11.2820512820513 40.3181818181818 3.57365702479339 1162.5 0.000600880152404055 0.0158740395101199 FALSE +ATP6V0A4 0.03 0.222701503353614 0.0495959595959596 2 0.0128205128205128 0.0909090909090909 7.09090909090909 886.5 0.336693018711006 0.799577485898251 FALSE +ATP6V0B 221.06 244.127008673019 59597.9963636364 79 180.5 364.863636363636 2.02140518761017 1235 0.00164679869283226 0.027428647080616 FALSE +ATP6V0C 14.14 16.3249947793393 266.505454545455 81 12.5769230769231 19.6818181818182 1.56491520711704 1122 0.0277112020859769 0.160923302769659 FALSE +ATP6V0CP3 0 0 0 0 0 0 NA 858 NaN NA NA +ATP6V0D1 53.25 95.2994615605848 9081.98737373737 45 38.2435897435897 106.454545454545 2.78359186907628 1201.5 0.001772293714077 0.0286014913746902 FALSE +ATP6V0D2 1.28 9.01522841831217 81.2743434343434 2 0 5.81818181818182 Inf 936 0.00783414581327792 0.0694811569640497 FALSE +ATP6V0E1 231.51 314.016003420272 98606.0504040404 76 207.653846153846 316.090909090909 1.52220108100827 1122.5 0.0269629537253602 0.157888927778971 FALSE +ATP6V0E2 190.01 242.477427669655 58795.3029292929 67 176.512820512821 237.863636363636 1.34757144366383 1054.5 0.0967125981983633 0.339774056935026 FALSE +ATP6V1A 22.6 57.9343062302798 3356.38383838384 33 17.2307692307692 41.6363636363636 2.4163961038961 1150 0.00372358602549614 0.0451310986741669 FALSE +ATP6V1B1 1.25 8.38152730712011 70.25 5 1.56410256410256 0.136363636363636 0.0871833084947839 851 0.886124495287814 1 FALSE +ATP6V1B2 54.85 108.729891906225 11822.1893939394 34 45.3333333333333 88.5909090909091 1.95421122994652 1125.5 0.00848964857782658 0.0734491329013889 FALSE +ATP6V1C1 46.06 84.8043285535246 7191.77414141414 38 44.1282051282051 52.9090909090909 1.19898579050235 964 0.314483040313195 0.77584878442132 FALSE +ATP6V1C2 0.19 1.21185224288519 1.46858585858586 5 0.0256410256410256 0.772727272727273 30.1363636363636 955 0.0334788253703192 0.182912165762671 FALSE +ATP6V1D 103.83 155.316233614656 24123.1324242424 56 89.7692307692308 153.681818181818 1.71196541247955 1021 0.157453470635775 0.48304748612535 FALSE +ATP6V1E1 35.47 74.7333921282173 5585.0798989899 34 36.2435897435897 32.7272727272727 0.902980994951281 851 0.948910058051973 1 FALSE +ATP6V1E2 0.53 4.73212746056468 22.3930303030303 2 0.67948717948718 0 0 836 0.460699420081267 0.916301306363014 FALSE +ATP6V1F 244.03 290.00255850491 84101.4839393939 87 190.858974358974 432.545454545455 2.26630922647581 1209 0.00350300768353415 0.0434722695426585 FALSE +ATP6V1G1 126.69 179.018180612749 32047.508989899 74 112.307692307692 177.681818181818 1.58209838107098 1176 0.00768663950230748 0.0694811569640497 FALSE +ATP6V1G2 1.78 10.3392749291527 106.900606060606 4 1.15384615384615 4 3.46666666666667 865.5 0.863785856235317 1 FALSE +ATP6V1G2-DDX39B 0 0 0 0 0 0 NA 858 NaN NA NA +ATP6V1G3 0 0 0 0 0 0 NA 858 NaN NA NA +ATP6V1H 32.61 86.8673544706369 7545.93727272727 34 20.2307692307692 76.5 3.78136882129278 1210.5 0.000520606261952447 0.01471868269444 FALSE +ATP7A 4.28 24.5587648161085 603.132929292929 8 3.16666666666667 8.22727272727273 2.59808612440191 923 0.253934656934114 0.673046438473734 FALSE +ATP7B 0.57 3.42968326128336 11.7627272727273 3 0.5 0.818181818181818 1.63636363636364 875 0.642227504899165 1 FALSE +ATP8A1 0.65 3.36462584408832 11.3207070707071 9 0.807692307692308 0.0909090909090909 0.112554112554113 807.5 0.401978508996738 0.871792826091711 FALSE +ATP8A2 0 0 0 0 0 0 NA 858 NaN NA NA +ATP8B1 5.46 23.043402175859 530.998383838384 8 6.01282051282051 3.5 0.582089552238806 868 0.866562196838596 1 FALSE +ATP8B2 0.1 0.643538199442282 0.414141414141414 4 0.0512820512820513 0.272727272727273 5.31818181818182 865.5 0.863782345348973 1 FALSE +ATP8B3 0.53 5.3 28.09 1 0.67948717948718 0 0 847 0.612193566468421 0.993316154786423 FALSE +ATP8B4 0.52 3.54332492373357 12.5551515151515 3 0.666666666666667 0 0 825 0.36014181863844 0.800436942927817 FALSE +ATP8B5P 0.03 0.171446607997765 0.0293939393939394 3 0.0256410256410256 0.0454545454545455 1.77272727272727 875 0.642181767836807 1 FALSE +ATP9A 20.45 50.1962562489887 2519.66414141414 32 20.2564102564103 21.1363636363636 1.04344073647871 944 0.390204649538973 0.852098145073051 FALSE +ATP9B 9.8 27.6599115521129 765.070707070707 21 9.7948717948718 9.81818181818182 1.00237981913375 966.5 0.206898023124575 0.579047208542656 FALSE +ATPAF1 63.66 116.482904628564 13568.2670707071 41 50.474358974359 110.409090909091 2.18742928394948 1149 0.00669556643871703 0.0647347318204911 FALSE +ATPAF1-AS1 0.6 6 36 1 0.769230769230769 0 0 847 0.612193566468421 0.993316154786423 FALSE +ATPAF2 5.63 29.5007806779085 870.296060606061 6 5.02564102564103 7.77272727272727 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22.3636363636364 12.7325812873258 954 0.0353712638595045 0.188711345632169 FALSE +G2E3 6.16 25.1153782018552 630.782222222222 21 3.82051282051282 14.4545454545455 3.78340451494814 982 0.148926699710893 0.466735457986902 FALSE +G3BP1 86.82 128.842349835414 16600.3511111111 64 61.1923076923077 177.681818181818 2.90366264784869 1273.5 0.000404969997351361 0.012634631372639 FALSE +G3BP2 17.67 45.3872351119906 2060.00111111111 37 19.1923076923077 12.2727272727273 0.63946073966114 950 0.379295552059485 0.832867737316862 FALSE +G6PC 0.01 0.1 0.01 1 0.0128205128205128 0 0 847 0.612193566468421 0.993316154786423 FALSE +G6PC2 0.07 0.7 0.49 1 0 0.318181818181818 Inf 897 0.0630558447149376 0.252399828906917 FALSE +G6PC3 58.78 120.300514285575 14472.2137373737 56 38.5897435897436 130.363636363636 3.37819389912413 1152.5 0.0105357818170194 0.0834576777966472 FALSE +G6PD 6.44 23.6341304306319 558.572121212121 13 2.23076923076923 21.3636363636364 9.57680250783699 1120 0.000196581793741831 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NA +GAGE12B 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12C 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12D 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12E 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12F 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12G 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12H 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12I 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE12J 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE13 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE2A 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE2B 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE2C 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE2D 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE2E 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE4 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE5 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE6 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE7 0 0 0 0 0 0 NA 858 NaN NA NA +GAGE8 0 0 0 0 0 0 NA 858 NaN NA NA +GAK 18 42.3570680302734 1794.12121212121 28 18.2051282051282 17.2727272727273 0.948783610755442 809.5 0.613910227015155 0.995761438384943 FALSE +GAL 1.49 14.4036295930764 207.464545454545 2 0.0641025641025641 6.54545454545455 102.109090909091 886.5 0.336693018711006 0.799577485898251 FALSE +GAL3ST1 0.03 0.3 0.09 1 0.0384615384615385 0 0 847 0.612193566468421 0.993316154786423 FALSE +GAL3ST2 0 0 0 0 0 0 NA 858 NaN NA NA +GAL3ST3 12.35 40.3232832457523 1625.96717171717 12 7.96153846153846 27.9090909090909 3.50548967940272 1071.5 0.00168806501417325 0.0277013365528093 FALSE +GAL3ST4 8.98 26.7362652363392 714.827878787879 21 6.96153846153846 16.1363636363636 2.31793068809643 885.5 0.752360945123209 1 FALSE +GALC 23.4 52.3108424939251 2736.42424242424 33 21.1794871794872 31.2727272727273 1.47655734096412 918.5 0.550459197069654 0.993316154786423 FALSE +GALE 11.59 34.1733829318975 1167.8201010101 19 6.35897435897436 30.1363636363636 4.7391862170088 1162.5 0.000219605945852989 0.00891991414714824 TRUE +GALK1 84.83 146.785217583414 21545.9001010101 49 72.3333333333333 129.136363636364 1.78529534981148 1022 0.144047295472255 0.455124013060527 FALSE +GALK2 9.94 29.8480393752329 890.905454545455 20 6.21794871794872 23.1363636363636 3.72089971883786 1048.5 0.0236283169137971 0.144775419694541 FALSE +GALM 5.38 22.1372121464326 490.056161616162 14 6.78205128205128 0.409090909090909 0.0603196425502664 795.5 0.392471164723297 0.856130301401142 FALSE +GALNS 35.44 78.0910269163397 6098.20848484848 32 13.3333333333333 113.818181818182 8.53636363636364 1412.5 2.58580026024812e-08 0.000158156330665433 TRUE +GALNT1 42.89 75.0755706813562 5636.34131313131 47 38.0897435897436 59.9090909090909 1.57284048835715 1035 0.111403015736112 0.3758685636329 FALSE +GALNT10 13.8 39.6835970999087 1574.78787878788 25 7.26923076923077 36.9545454545455 5.08369408369408 1243 2.57936854315859e-05 0.00333009304511215 TRUE +GALNT11 48.29 100.040930512355 10008.1877777778 47 42.7435897435897 67.9545454545455 1.58981839995637 1138.5 0.0115564913904525 0.0885231569303789 FALSE +GALNT12 0.14 1.4 1.96 1 0 0.636363636363636 Inf 897 0.0630558447149376 0.252399828906917 FALSE +GALNT13 8.34 38.0823721780441 1450.26707070707 11 7.93589743589744 9.77272727272727 1.23145836393009 935 0.241233346787172 0.64693188935981 FALSE +GALNT14 0 0 0 0 0 0 NA 858 NaN NA NA +GALNT2 59.04 97.9722615866554 9598.56404040404 57 38.8205128205128 130.727272727273 3.36747928425603 1157 0.00963062418874833 0.0791866382979138 FALSE +GALNT3 1.75 9.24784987295573 85.5227272727273 5 2.12820512820513 0.409090909090909 0.192223439211391 852 0.903548412148226 1 FALSE +GALNT4 0.01 0.1 0.01 1 0.0128205128205128 0 0 847 0.612193566468421 0.993316154786423 FALSE +GALNT5 0.68 5.05101249975956 25.5127272727273 4 0.243589743589744 2.22727272727273 9.14354066985646 963.5 0.0100698575199179 0.0809903585281367 FALSE +GALNT6 0.04 0.242878362539562 0.058989898989899 3 0.0384615384615385 0.0454545454545455 1.18181818181818 874.5 0.652332847318063 1 FALSE +GALNT7 4.99 18.2200328199374 331.969595959596 15 3.84615384615385 9.04545454545454 2.35181818181818 894.5 0.629650669233521 1 FALSE +GALNT8 0.07 0.7 0.49 1 0.0897435897435897 0 0 847 0.612193566468421 0.993316154786423 FALSE +GALNT9 0 0 0 0 0 0 NA 858 NaN NA NA +GALNTL1 12.02 74.4072848611212 5536.44404040404 8 14 5 0.357142857142857 821.5 0.524298689622566 0.993316154786423 FALSE +GALNTL2 12.21 40.5737375874861 1646.22818181818 15 12.0897435897436 12.6363636363636 1.0452135351393 845 0.867028253424351 1 FALSE +GALNTL4 13.81 59.2826980056431 3514.43828282828 13 11.5512820512821 21.8181818181818 1.88881041267279 1011 0.029903060298138 0.169072033159179 FALSE +GALNTL5 0 0 0 0 0 0 NA 858 NaN NA NA +GALNTL6 0.1 1 1 1 0.128205128205128 0 0 847 0.612193566468421 0.993316154786423 FALSE +GALP 0.13 1.3 1.69 1 0.166666666666667 0 0 847 0.612193566468421 0.993316154786423 FALSE +GALR1 1.07 10.7 114.49 1 1.37179487179487 0 0 847 0.612193566468421 0.993316154786423 FALSE +GALR2 0.06 0.6 0.36 1 0 0.272727272727273 Inf 897 0.0630558447149376 0.252399828906917 FALSE +GALR3 0 0 0 0 0 0 NA 858 NaN NA NA +GALT 27.1 114.577881412997 13128.0909090909 21 33.1410256410256 5.68181818181818 0.171443643397222 771 0.312076004281692 0.771947927178425 FALSE +GAMT 37.21 62.5457077308712 3911.96555555556 48 30.8846153846154 59.6363636363636 1.9309407902185 1104 0.0275525056136955 0.160283390490255 FALSE +GAN 2.32 12.8541782697261 165.229898989899 6 2.83333333333333 0.5 0.176470588235294 841.5 0.746358481014544 1 FALSE +GANAB 139.69 205.787607238457 42348.5392929293 70 92.9358974358974 305.454545454545 3.28672293357077 1342 4.52865750367076e-05 0.00431711856705584 TRUE +GANC 8.9 37.034654805542 1371.56565656566 15 9.84615384615385 5.54545454545455 0.563210227272727 842 0.835526728399617 1 FALSE +GAP43 312.81 472.032114448484 222814.317070707 67 206.628205128205 689.272727272727 3.33581142441352 1321 8.87470359612381e-05 0.00568175544203346 TRUE +GAPDH 5814.1 6338.31228611873 40174202.6363636 98 4537.19230769231 10341.3181818182 2.27923294419009 1399 6.87667914974894e-06 0.0017676947702765 TRUE +GAPDHS 0.56 5.49989898897142 30.2488888888889 2 0.717948717948718 0 0 836 0.460699420081267 0.916301306363014 FALSE +GAPT 0 0 0 0 0 0 NA 858 NaN NA NA +GAPVD1 24.83 58.101627265586 3375.79909090909 34 22.8461538461538 31.8636363636364 1.39470462197735 948.5 0.374963116738437 0.825286466639586 FALSE +GAR1 9.4 33.5083285290102 1122.80808080808 22 5.83333333333333 22.0454545454545 3.77922077922078 1018.5 0.0662586218876693 0.259344947980821 FALSE +GARNL3 13.74 58.1224100107226 3378.21454545455 17 13.8846153846154 13.2272727272727 0.952656761521027 966 0.17165065128648 0.512015881958446 FALSE +GARS 88.4 161.383037672752 26044.4848484848 58 66.2564102564103 166.909090909091 2.51913875598086 1069 0.0687087650336074 0.266575862743705 FALSE +GART 42.39 72.4140584319499 5243.79585858586 50 32.5128205128205 77.4090909090909 2.3808789790651 1144.5 0.0109540120202733 0.0856196389484596 FALSE +GAS1 7.75 27.639590621009 763.94696969697 14 8.1025641025641 6.5 0.802215189873418 943 0.243828970671638 0.652070884258965 FALSE +GAS2 0.2 1.53082799276547 2.34343434343434 4 0 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