| Previous changeset 0:cf2fa609625b (2017-11-26) Next changeset 2:5cdffe94464e (2018-03-08) |
|
Commit message:
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty |
|
modified:
expression_rnaseq_abbased.xml |
|
added:
README.rst test-data/Get_annotation_RNAseq.txt test-data/ID_Converter_Lacombe_et_al_2017_OK.txt |
| b |
| diff -r cf2fa609625b -r 8dd24f13f923 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 16 04:09:32 2018 -0500 |
| b |
| @@ -0,0 +1,50 @@ +Wrapper for Get annotation from RNAseq/Ab-based experiments (Human species) tool +========================= + +**Authors** + +Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + +========================= + +This tool adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list. + +**Input** + +Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs. + +**Databases** + +HPA source file: http://www.proteinatlas.org/download/proteinatlas.tab.gz + +**Annotation** + +- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) + +- Gene description: entry description (full text) + +- Evidence: at protein level, at transcript level or no evidence + +- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF + +- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna . + +- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if . + +- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih . + +- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa + +- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. + +- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. + +**Outputs** + +The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. \ No newline at end of file |
| b |
| diff -r cf2fa609625b -r 8dd24f13f923 expression_rnaseq_abbased.xml --- a/expression_rnaseq_abbased.xml Sun Nov 26 20:49:17 2017 -0500 +++ b/expression_rnaseq_abbased.xml Fri Feb 16 04:09:32 2018 -0500 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="rna_abbased_data" name="Expression from RNAseq/Ab-based data (Human Protein Atlas)" version="0.1.0">\n+<tool id="rna_abbased_data" name="Get annotation from RNAseq/Ab-based experiments (Human species)" version="0.1.0">\n <description>\n </description>\n <requirements>\n@@ -23,31 +23,31 @@\n \n <inputs>\n <conditional name="inputtype">\n- <param name="filetype" type="select" label="Select your type of input file"> \n- <option value="file_all">Input file containing your identifiers</option>\n+ <param name="filetype" type="select" label="Enter your list of Ensembl gene ID"> \n+ <option value="file_all">Input file containing your IDs</option>\n <option value="copy_paste">Copy/paste your list of IDs</option> \n </param>\n <when value="copy_paste">\n <param name="genelist" type="text" label="Enter a list of identifiers"/>\n </when>\n <when value="file_all">\n- <param name="genelist" type="data" format="txt,tabular" label="Choose a multiple-columns file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>\n- <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/> \n+ <param name="genelist" type="data" format="txt,tabular" label="Choose your file" help="This file must imperatively have 1 column filled with Ensembl Gene IDs (ENSG). Please use the ID_Converter tool if this is not the case."/>\n+ <param name="column" type="text" label="Please specify the column where are your Ensembl gene IDs (e.g : Enter c1 if ENSG ID are in column n\xc2\xb01)" value="c1"/> \n <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> \n \t\t <option value="TRUE" selected="true">Yes</option>\n <option value="FALSE" selected="false">No</option>\n </param>\n </when>\n </conditional>\n- <section name="options" title="RNAseq/Ab-based data expression options" expanded="True"> \n- <param name="hpaparams" type="select" label="Choose the expression from RNAseq/ab-based data you would like to add to your input" multiple="True" display="checkboxes"> \n+ <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> \n+ <param name="hpaparams" type="select" label="Choose the information from RNAseq/ab-based data you want to add to your list (see below for details)" multiple="True" display="checkboxes"> \n <option value="Gene" selected="true">Gene name</option>\n <option value="Gene.description" selected="false">Gene description</option>\n <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>\n <option value="Antibody">Antibody reference</option>\n <option value="RNA.tissue.category">RNA tissue category</option>\n- \t\t <option value="Reliability..IH.">IH detection level</option>\n- <option value="Reliability..IF.">IF detection level</option>\n+ \t\t <option value="Reliability.IH">IH detection level</option>\n+ <option value="Reliability.IF">IF detection level</option>\n <option value="Subcellular.location">Subcellular location</option>\n <option value="RNA.TS.TPM">RNA tissue specificity abundance in \'Transcript Per Million\'</option>\n <option value="TPM.max.in.non.specific">RNA non-specific tissue abundance in \'Transcript Per Million\'</option>\n@@ -58,65 +58,76 @@\n \n \n <outputs>\n- <data name="output" format="tabular" label="abc"/>\n+ <data name="output" format="tabular" label=""/>\n </outputs>\n \n <tests>\n <test>\n <conditional name="inputtype">\n <param name="filetype " value="file_all"/>\n- <param name="genelist" value="mitochondrion_enzymes_Nextprot.txt"/>\n- <param name="column" value="c1"/>\n+ <param name="genelist" value="ID_Converter_Laco'..b"he Human Protein Atlas webservice. Pertinent information, such as tissular location, will be added for each gene to your input file. \n+**Annotation**\n+\n+- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) \n \n-- HPA cancer tissue : will filter the input according to the data contained in the Human Protein Atlas webservice for cancer. Pertinent information, such as tumor type, will be added for each gene to your input file. \n+- Gene description: entry description (full text) \n \n-**Parameters**\n+- Evidence: at protein level, at transcript level or no evidence\n \n-For HPA normal tissue :\n+- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF\n \n-- tissue category : categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .\n+- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .\n \n-- level of detection IF : level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .\n+- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .\n+\n+- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih .\n \n-- level of detection IH : level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .\n+- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa\n \n-For HPA cancer tissue : \n+- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts.\n \n-- tumors : which tumors are associated with your protein-coding genes according to the Human Protein Atlas.\n-\n+- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.\n \n **Outputs**\n \n-The output will be a tabular file. The initial columns will be kept, but lines can be deleted due to the filtering process. Additional columns will be added according to which data you chose to filter your input with. \n+The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. \n+\n+-----\n \n+.. class:: infomark\n+\n+**Authors**\n \n-**Data sources**\n+Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR\n+\n+Sandra D\xc3\xa9rozier, Olivier Ru\xc3\xa9, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform\n \n-The data for HPA normal tissue was retrieved from the Human Protein Atlas downloadable data repository (http://www.proteinatlas.org/download/proteinatlas.tab.gz).\n+This work has been partially funded through the French National Agency for Research (ANR) IFB project.\n \n-The data for HPA cancer was retrieved from the Human Protein Atlas downloadable data repository (http://www.proteinatlas.org/download/cancer.csv.zip).\n+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.\n+\n ]]></help>\n \n <citations>\n" |
| b |
| diff -r cf2fa609625b -r 8dd24f13f923 test-data/Get_annotation_RNAseq.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Get_annotation_RNAseq.txt Fri Feb 16 04:09:32 2018 -0500 |
| b |
| b'@@ -0,0 +1,152 @@\n+Ensembl gene ids\tProtein.accession.number..UniProt.\tProtein.name\tNumber.of.peptides..razor...unique.\tneXtProt_ID\tUniProt.ID\tGeneID\tMIM\tGene\tGene.description\tEvidence\tAntibody\tRNA.tissue.category\tSubcellular.location\tRNA.TS.TPM\tTPM.max.in.non.specific\n+ENSG00000005893\tP13473\tLysosome-associated membrane glycoprotein 2\t2\tNX_P13473\tLAMP2_HUMAN\t3920\t300257; 309060\tLAMP2\tLysosomal-associated membrane protein 2\tEvidence at protein level\tCAB005272, HPA029100\tExpressed in all\tNA\tNA\tgallbladder: 223.9\n+ENSG00000006625\tO75223\tGamma-glutamylcyclotransferase\t6\tNX_O75223\tGGCT_HUMAN\t79017\t137170\tGGCT\tGamma-glutamylcyclotransferase\tEvidence at protein level\tHPA020735, HPA029914\tExpressed in all\tNA\tNA\tepididymis: 123.9\n+ENSG00000012223\tP02788\tLactotransferrin\t21\tNX_P02788\tTRFL_HUMAN\t4057\t150210\tLTF\tLactotransferrin\tEvidence at protein level\tCAB008646, CAB016201, HPA057177, HPA059976\tTissue enhanced\tNA\tbone marrow: 2808.6;cervix, uterine: 1024.2\tseminal vesicle: 526.7\n+ENSG00000014216\tP07384\tCalpain-1 catalytic subunit\t4\tNX_P07384\tCAN1_HUMAN\t823\t114220; 616907\tCAPN1\tCalpain 1, (mu/I) large subunit\tEvidence at protein level\tHPA005992\tExpressed in all\tCytosol\tNA\tesophagus: 245.3\n+ENSG00000021355\tP30740\tLeukocyte elastase inhibitor\t3\tNX_P30740\tILEU_HUMAN\t1992\t130135\tSERPINB1\tSerpin peptidase inhibitor, clade B (ovalbumin), member 1\tEvidence at protein level\tHPA018871, HPA052642\tExpressed in all\tNA\tNA\tesophagus: 466.2\n+ENSG00000025708\tP19971\tThymidine phosphorylase\t2\tNX_P19971\tTYPH_HUMAN\t1890\t131222; 603041\tTYMP\tThymidine phosphorylase\tEvidence at protein level\tHPA000530, HPA001072, CAB002518\tTissue enhanced\tNuclear bodies<br>Golgi apparatus\tappendix: 103.2\tspleen: 54.0\n+ENSG00000035403\tP18206\tVinculin\t4\tNX_P18206\tVINC_HUMAN\t7414\t193065; 611407; 613255\tVCL\tVinculin\tEvidence at protein level\tHPA002131, CAB002453, HPA063777\tExpressed in all\tFocal adhesion sites\tNA\tsmooth muscle: 339.0\n+ENSG00000038002\tP20933\tN(4)-(beta-N-acetylglucosaminyl)-L-asparaginase\t3\tNX_P20933\tASPG_HUMAN\t175\t208400; 613228\tAGA\tAspartylglucosaminidase\tEvidence at protein level\tHPA031415, HPA031417\tExpressed in all\tNA\tNA\tepididymis: 34.7\n+ENSG00000042493\tP40121\tMacrophage-capping protein\t2\tNX_P40121\tCAPG_HUMAN\t822\t153615\tCAPG\tCapping protein (actin filament), gelsolin-like\tEvidence at protein level\tHPA018843, HPA019080, HPA019092\tExpressed in all\tNucleus\tNA\tparathyroid gland: 233.4\n+ENSG00000044574\tP11021\t78 kDa glucose-regulated protein\t10\tNX_P11021\tGRP78_HUMAN\t3309\t138120\tHSPA5\tHeat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)\tEvidence at protein level\tCAB005221, HPA038845, HPA038846\tExpressed in all\tCytosol\tNA\tthyroid gland: 965.5\n+ENSG00000057149\tP29508\tSerpin B3\t20\tNX_P29508\tSPB3_HUMAN\t6317\t600517\tSERPINB3\tSerpin peptidase inhibitor, clade B (ovalbumin), member 3\tEvidence at protein level\tCAB018772, CAB036006, CAB036007, HPA048341, HPA049988, HPA055992\tGroup enriched\tPlasma membrane<br>Cytosol\tcervix, uterine: 297.6;esophagus: 851.2\turinary bladder: 90.5\n+ENSG00000057608\tP50395\tRab GDP dissociation inhibitor beta\t2\tNX_P50395\tGDIB_HUMAN\t2665\t600767\tGDI2\tGDP dissociation inhibitor 2\tEvidence at protein level\tHPA049290, HPA057668\tExpressed in all\tNA\tNA\tlymph node: 244.2\n+ENSG00000067225\tP14618\tPyruvate kinase PKM\t9\tNX_P14618\tKPYM_HUMAN\t5315\t179050\tPKM\tPyruvate kinase, muscle\tEvidence at protein level\tCAB019421, HPA029501\tExpressed in all\tCytosol\tNA\tskeletal muscle: 1492.7\n+ENSG00000074800\tP06733\tAlpha-enolase\t15\tNX_P06733\tENOA_HUMAN\t2023\t172430\tENO1\tEnolase 1, (alpha)\tEvidence at protein level\tCAB018614, HPA068284, CAB069394\tExpressed in all\tNucleoplasm<br>Plasma membrane<br>Cytosol\tNA\tappendix: 789.1\n+ENSG00000077549\tP47756\tF-actin-capping protein subunit beta\t2\tNX_P47756\tCAPZB_HUMAN\t832\t601572\tCAPZB\tCapping protein (actin filament) muscle Z-line, beta\tEvidence at protein level\tHPA031531, HPA056066\tExpressed in all\tNucleoplasm<br>Vesicles<br>Cytosol\tNA\tsmooth muscle: 484.4\n+ENSG00000080824\tP07900\tHeat shock protein HSP 90-alpha\t6\tNX_P07900\tHS9'..b'rotein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+ENSG00000211895; ENSG00000282633\tP01876\tIg alpha-1 chain C region\t16\tNX_P01876\tIGHA1_HUMAN\tNA\t146900\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+ENSG00000211896; ENSG00000277633\tP01857\tIg gamma-1 chain C region\t7\tNX_P01857\tIGHG1_HUMAN\tNA\t147100; 254500\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+ENSG00000211899; ENSG00000282657\tP01871\tIg mu chain C region\t2\tNX_P01871\tIGHM_HUMAN\tNA\t147020; 601495\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+ENSG00000211942; ENSG00000282286\tP01766\tIg heavy chain V-III region BRO\t2\tNX_P01766\tHV313_HUMAN\tNA\tNA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+ENSG00000221983\tP62987\tUbiquitin-60S ribosomal protein L40\t6\tNX_P62987\tRL40_HUMAN\t7311\t191321\tUBA52\tUbiquitin A-52 residue ribosomal protein fusion product 1\tEvidence at protein level\tHPA041344, HPA049132, HPA056624\tExpressed in all\tNucleoplasm<br>Endoplasmic reticulum<br>Plasma membrane<br>Cytosol\tNA\tovary: 1909.1\n+ENSG00000229314\tP02763\tAlpha-1-acid glycoprotein 1\t3\tNX_P02763\tA1AG1_HUMAN\t5004\t138600\tORM1\tOrosomucoid 1\tEvidence at protein level\tCAB006265, HPA046438, HPA047725, HPA057726\tTissue enriched\tGolgi apparatus<br>Vesicles\tliver: 10546.0\tbone marrow: 152.7\n+ENSG00000241553\tP59998\tActin-related protein 2/3 complex subunit 4\t2\tNX_P59998\tARPC4_HUMAN\t10093\t604226\tARPC4\tActin related protein 2/3 complex, subunit 4, 20kDa\tEvidence at protein level\tNA\tExpressed in all\tNA\tNA\tlymph node: 167.0\n+ENSG00000244734\tP68871\tHemoglobin subunit beta\t4\tNX_P68871\tHBB_HUMAN\t3043\t140700; 141900; 603902; 603903; 611162; 613985\tHBB\tHemoglobin, beta\tEvidence at protein level\tCAB009526, HPA043234\tTissue enriched\tNA\tbone marrow: 78261.0\tplacenta: 8978.3\n+ENSG00000254772\tP26641\tElongation factor 1-gamma\t3\tNX_P26641\tEF1G_HUMAN\t1937\t130593\tEEF1G\tEukaryotic translation elongation factor 1 gamma\tEvidence at protein level\tHPA040688\tExpressed in all\tMitochondria\tNA\tovary: 2987.8\n+ENSG00000257017\tP00738\tHaptoglobin\t3\tNX_P00738\tHPT_HUMAN\t3240\t140100; 614081\tHP\tHaptoglobin\tEvidence at protein level\tCAB003787, HPA047750\tTissue enriched\tVesicles\tliver: 28321.0\tbone marrow: 156.1\n+ENSG00000277791; ENSG00000275903\tP49720\tProteasome subunit beta type-3\t2\tNX_P49720\tPSB3_HUMAN\t5691\t602176\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+ENSG00000281123\tQ9Y6R7\tIgGFc-binding protein\t3\tNX_Q9Y6R7\tFCGBP_HUMAN\t8857\t617553\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\tProtein not found in HPA\n+NA\tP01834\tIg kappa chain C region\t8\tNX_P01834\tIGKC_HUMAN\tNA\t147200; 614102\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+NA\tP01860\tIg gamma-3 chain C region\t2\tNX_P01860\tIGHG3_HUMAN\tNA\t147120\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+NA\tP58107\tEpiplakin\t5\tNX_P58107\tEPIPL_HUMAN\t83481\t607553\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+NA\tP01625\tIg kappa chain V-IV region Len\t2\tNA\tNA\tNA\tNA\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+NA\tP0CG05\tIg lambda-2 chain C regions\t4\tNA\tNA\tNA\tNA\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+NA\tP01623\tIg kappa chain V-III region\t3\tNA\tNA\tNA\tNA\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n+NA\tP01765\tIg heavy chain V-III region TIL\t2\tNA\tNA\tNA\tNA\tGRPEL2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n' |
| b |
| diff -r cf2fa609625b -r 8dd24f13f923 test-data/ID_Converter_Lacombe_et_al_2017_OK.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ID_Converter_Lacombe_et_al_2017_OK.txt Fri Feb 16 04:09:32 2018 -0500 |
| b |
| b'@@ -0,0 +1,152 @@\n+Protein accession number (UniProt)\tProtein name\tNumber of peptides (razor + unique)\tneXtProt_ID\tUniProt.ID\tGeneID\tMIM\tEnsembl\n+P15924\tDesmoplakin\t69\tNX_P15924\tDESP_HUMAN\t1832\t125647; 605676; 607450; 607655; 609638; 612908; 615821\tENSG00000096696\n+P02538\tKeratin, type II cytoskeletal 6A\t53\tNX_P02538\tK2C6A_HUMAN\t3853\t148041; 615726\tENSG00000205420\n+P02768\tSerum albumin\t44\tNX_P02768\tALBU_HUMAN\t213\t103600; 615999; 616000\tENSG00000163631\n+P08779\tKeratin, type I cytoskeletal 16\t29\tNX_P08779\tK1C16_HUMAN\t3868\t148067; 167200; 613000\tENSG00000186832\n+Q02413\tDesmoglein-1\t24\tNX_Q02413\tDSG1_HUMAN\t1828\t125670; 148700; 615508\tENSG00000134760\n+P07355\tAnnexin A2;Putative annexin A2-like protein\t22\tNX_P07355\tANXA2_HUMAN\t302\t151740\tENSG00000182718\n+P14923\tJunction plakoglobin\t22\tNX_P14923\tPLAK_HUMAN\t3728\t173325; 601214; 611528\tENSG00000173801\n+P02788\tLactotransferrin\t21\tNX_P02788\tTRFL_HUMAN\t4057\t150210\tENSG00000012223\n+Q9HC84\tMucin-5B\t21\tNX_Q9HC84\tMUC5B_HUMAN\t727897\t178500; 600770\tENSG00000117983\n+P29508\tSerpin B3\t20\tNX_P29508\tSPB3_HUMAN\t6317\t600517\tENSG00000057149\n+P63261\tActin, cytoplasmic 2\t19\tNX_P63261\tACTG_HUMAN\t71\t102560; 604717; 614583\tENSG00000184009\n+Q8N1N4\tKeratin, type II cytoskeletal 78\t18\tNX_Q8N1N4\tK2C78_HUMAN\t196374\t611159\tENSG00000170423\n+Q04695\tKeratin, type I cytoskeletal 17\t18\tNX_Q04695\tK1C17_HUMAN\t3872\t148069; 167210; 184500\tENSG00000128422\n+P01876\tIg alpha-1 chain C region\t16\tNX_P01876\tIGHA1_HUMAN\tNA\t146900\tENSG00000211895; ENSG00000282633\n+Q01469\tFatty acid-binding protein 5, epidermal\t15\tNX_Q01469\tFABP5_HUMAN\t2171\t605168\tENSG00000164687\n+P31944\tCaspase-14\t15\tNX_P31944\tCASPE_HUMAN\t23581\t605848; 617320\tENSG00000105141\n+P01833\tPolymeric immunoglobulin receptor\t15\tNX_P01833\tPIGR_HUMAN\t5284\t173880\tENSG00000162896\n+P06733\tAlpha-enolase\t15\tNX_P06733\tENOA_HUMAN\t2023\t172430\tENSG00000074800\n+P25311\tZinc-alpha-2-glycoprotein\t15\tNX_P25311\tZA2G_HUMAN\t563\t194460\tENSG00000160862\n+Q15149\tPlectin\t15\tNX_Q15149\tPLEC_HUMAN\t5339\t131950; 226670; 601282; 612138; 613723; 616487\tENSG00000178209\n+P19013\tKeratin, type II cytoskeletal 4\t13\tNX_P19013\tK2C4_HUMAN\tNA\t123940; 193900\tENSG00000170477\n+Q6KB66\tKeratin, type II cytoskeletal 80\t13\tNX_Q6KB66\tK2C80_HUMAN\t144501\t611161\tENSG00000167767\n+Q08188\tProtein-glutamine gamma-glutamyltransferase E\t12\tNX_Q08188\tTGM3_HUMAN\t7053\t600238; 617251\tENSG00000125780\n+P13646\tKeratin, type I cytoskeletal 13\t11\tNX_P13646\tK1C13_HUMAN\t3860\t148065; 615785\tENSG00000171401\n+Q86YZ3\tHornerin\t11\tNX_Q86YZ3\tHORN_HUMAN\t388697\t616293\tENSG00000197915\n+P04259\tKeratin, type II cytoskeletal 6B\t10\tNX_P04259\tK2C6B_HUMAN\t3854\t148042; 615728\tENSG00000185479\n+P02545\tPrelamin-A/C;Lamin-A/C\t10\tNX_P02545\tLMNA_HUMAN\t4000\t115200; 150330; 151660; 159001; 176670; 181350; 212112; 248370; 275210; 605588; 610140; 613205; 616516\tENSG00000160789\n+P04083\tAnnexin A1\t10\tNX_P04083\tANXA1_HUMAN\t301\t151690\tENSG00000135046\n+P11021\t78 kDa glucose-regulated protein\t10\tNX_P11021\tGRP78_HUMAN\t3309\t138120\tENSG00000044574\n+P02787\tSerotransferrin\t9\tNX_P02787\tTRFE_HUMAN\t7018\t190000; 209300\tENSG00000091513\n+P04040\tCatalase\t9\tNX_P04040\tCATA_HUMAN\t847\t115500; 614097\tENSG00000121691\n+P31151\tProtein S100-A7\t9\tNX_P31151\tS10A7_HUMAN\t6278\t600353\tENSG00000143556\n+P31947\t14-3-3 protein sigma\t9\tNX_P31947\t1433S_HUMAN\t2810\t601290\tENSG00000175793\n+Q96P63\tSerpin B12\t9\tNX_Q96P63\tSPB12_HUMAN\t89777\t615662\tENSG00000166634\n+P14618\tPyruvate kinase PKM\t9\tNX_P14618\tKPYM_HUMAN\t5315\t179050\tENSG00000067225\n+P60174\tTriosephosphate isomerase\t9\tNX_P60174\tTPIS_HUMAN\t7167\t190450; 615512\tENSG00000111669\n+Q06830\tPeroxiredoxin-1\t9\tNX_Q06830\tPRDX1_HUMAN\t5052\t176763\tENSG00000117450\n+P01040\tCystatin-A\t8\tNX_P01040\tCYTA_HUMAN\t1475\t184600; 607936\tENSG00000121552\n+P05089\tArginase-1\t8\tNX_P05089\tARGI1_HUMAN\t383\t207800; 608313\tENSG00000118520\n+P01834\tIg kappa chain C region\t8\tNX_P01834\tIGKC_HUMAN\tNA\t147200; 614102\tNA\n+P04406\tGlyceraldehyde-3-phosphate dehydrogenase\t8\tNX_P04406\tG3P_HUMAN\t2597\t138400\tENSG00000111640\n+P0DMV9\tHeat shock 70 kDa protein 1B\t8\tNX_P0DMV9\tHS71B_HUMAN\t3303; 3304\t140550; '..b'X_P36952\tSPB5_HUMAN\t5268\t154790\tENSG00000206075\n+P40926\tMalate dehydrogenase, mitochondrial\t3\tNX_P40926\tMDHM_HUMAN\t4191\t154100; 617339\tENSG00000146701\n+Q9Y6R7\tIgGFc-binding protein\t3\tNX_Q9Y6R7\tFCGBP_HUMAN\t8857\t617553\tENSG00000281123\n+O95274\tLy6/PLAUR domain-containing protein 3\t2\tNX_O95274\tLYPD3_HUMAN\t27076\t609484\tENSG00000124466\n+P00491\tPurine nucleoside phosphorylase\t2\tNX_P00491\tPNPH_HUMAN\t4860\t164050; 613179\tENSG00000198805\n+P04080\tCystatin-B\t2\tNX_P04080\tCYTB_HUMAN\t1476\t254800; 601145\tENSG00000160213\n+P09972\tFructose-bisphosphate aldolase C\t2\tNX_P09972\tALDOC_HUMAN\t230\t103870\tENSG00000109107\n+P19012\tKeratin, type I cytoskeletal 15\t2\tNX_P19012\tK1C15_HUMAN\t3866\t148030\tENSG00000171346\n+P20930\tFilaggrin\t2\tNX_P20930\tFILA_HUMAN\t2312\t135940; 146700; 605803\tENSG00000143631\n+Q96FX8\tp53 apoptosis effector related to PMP-22\t2\tNX_Q96FX8\tPERP_HUMAN\t64065\t609301\tENSG00000112378\n+Q9UIV8\tSerpin B13\t2\tNX_Q9UIV8\tSPB13_HUMAN\t5275\t604445\tENSG00000197641\n+P01625\tIg kappa chain V-IV region Len\t2\tNA\tNA\tNA\tNA\tNA\n+P01765\tIg heavy chain V-III region TIL\t2\tNA\tNA\tNA\tNA\tNA\n+P01766\tIg heavy chain V-III region BRO\t2\tNX_P01766\tHV313_HUMAN\tNA\tNA\tENSG00000211942; ENSG00000282286\n+P01860\tIg gamma-3 chain C region\t2\tNX_P01860\tIGHG3_HUMAN\tNA\t147120\tNA\n+P01871\tIg mu chain C region\t2\tNX_P01871\tIGHM_HUMAN\tNA\t147020; 601495\tENSG00000211899; ENSG00000282657\n+P05090\tApolipoprotein D\t2\tNX_P05090\tAPOD_HUMAN\t347\t107740\tENSG00000189058\n+P06870\tKallikrein-1\t2\tNX_P06870\tKLK1_HUMAN\t3816\t147910; 615953\tENSG00000167748\n+P07858\tCathepsin B\t2\tNX_P07858\tCATB_HUMAN\t1508\t116810\tENSG00000164733\n+P08865\t40S ribosomal protein SA\t2\tNX_P08865\tRSSA_HUMAN\t3921\t150370; 271400\tENSG00000168028\n+P11279\tLysosome-associated membrane glycoprotein 1\t2\tNX_P11279\tLAMP1_HUMAN\t3916\t153330\tENSG00000185896\n+P13473\tLysosome-associated membrane glycoprotein 2\t2\tNX_P13473\tLAMP2_HUMAN\t3920\t300257; 309060\tENSG00000005893\n+P19971\tThymidine phosphorylase\t2\tNX_P19971\tTYPH_HUMAN\t1890\t131222; 603041\tENSG00000025708\n+P23284\tPeptidyl-prolyl cis-trans isomerase B\t2\tNX_P23284\tPPIB_HUMAN\t5479\t123841; 259440\tENSG00000166794\n+P23396\t40S ribosomal protein S3\t2\tNX_P23396\tRS3_HUMAN\t6188\t600454\tENSG00000149273\n+P25705\tATP synthase subunit alpha, mitochondrial\t2\tNX_P25705\tATPA_HUMAN\t498\t164360; 615228; 616045\tENSG00000152234\n+P27482\tCalmodulin-like protein 3\t2\tNX_P27482\tCALL3_HUMAN\t810\t114184\tENSG00000178363\n+P31949\tProtein S100-A11\t2\tNX_P31949\tS10AB_HUMAN\t6282\t603114\tENSG00000163191\n+P40121\tMacrophage-capping protein\t2\tNX_P40121\tCAPG_HUMAN\t822\t153615\tENSG00000042493\n+P42357\tHistidine ammonia-lyase\t2\tNX_P42357\tHUTH_HUMAN\t3034\t235800; 609457\tENSG00000084110\n+P47756\tF-actin-capping protein subunit beta\t2\tNX_P47756\tCAPZB_HUMAN\t832\t601572\tENSG00000077549\n+P48637\tGlutathione synthetase\t2\tNX_P48637\tGSHB_HUMAN\t2937\t231900; 266130; 601002\tENSG00000100983\n+P49720\tProteasome subunit beta type-3\t2\tNX_P49720\tPSB3_HUMAN\t5691\t602176\tENSG00000277791; ENSG00000275903\n+P50395\tRab GDP dissociation inhibitor beta\t2\tNX_P50395\tGDIB_HUMAN\t2665\t600767\tENSG00000057608\n+P59998\tActin-related protein 2/3 complex subunit 4\t2\tNX_P59998\tARPC4_HUMAN\t10093\t604226\tENSG00000241553\n+P61160\tActin-related protein 2\t2\tNX_P61160\tARP2_HUMAN\t10097\t604221\tENSG00000138071\n+P61916\tEpididymal secretory protein E1\t2\tNX_P61916\tNPC2_HUMAN\t10577\t601015; 607625\tENSG00000119655\n+P04745\tAlpha-amylase 1\t23\tNX_P04745\tAMY1_HUMAN\t276; 277; 278\t104700; 104701; 104702\tENSG00000174876; ENSG00000187733; ENSG00000237763\n+Q9NZT1\tCalmodulin-like protein 5\t8\tNX_Q9NZT1\tCALL5_HUMAN\t51806\t605183\tENSG00000178372\n+P12273\tProlactin-inducible protein\t6\tNX_P12273\tPIP_HUMAN\t5304\t176720\tENSG00000159763\n+Q96DA0\tZymogen granule protein 16 homolog B\t5\tNX_Q96DA0\tZG16B_HUMAN\t124220\tNA\tENSG00000162078; ENSG00000283056\n+P01036\tCystatin-S\t5\tNX_P01036\tCYTS_HUMAN\t1472\t123857\tENSG00000101441\n+Q8TAX7\tMucin-7\t2\tNX_Q8TAX7\tMUC7_HUMAN\t4589\t158375; 600807\tENSG00000171195\n+P01037\tCystatin-SN\t2\tNX_P01037\tCYTN_HUMAN\t1469\t123855\tENSG00000170373\n+P09228\tCystatin-SA\t2\tNX_P09228\tCYTT_HUMAN\t1470\t123856\tENSG00000170369\n' |