| Previous changeset 13:0b279190f90d (2019-06-28) Next changeset 15:208b87582b4c (2020-04-29) |
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Commit message:
"planemo upload commit c4edbc8a0ffd86395f088cb5b6592f77db658ac7" |
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modified:
add_expression_HPA.R add_expression_data.xml |
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added:
proteore_protein_full_atlas.loc.sample tool-data/HPA_full_atlas_23-10-2018.tsv tool_data_table_conf.xml.sample |
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removed:
proteinatlas.csv |
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| diff -r 0b279190f90d -r 133309fd6875 add_expression_HPA.R --- a/add_expression_HPA.R Fri Jun 28 05:01:37 2019 -0400 +++ b/add_expression_HPA.R Fri Jan 24 04:22:48 2020 -0500 |
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| @@ -146,6 +146,13 @@ } } +convert_to_previous_header <- function(options){ + header = c('Gene','description','Evidence','Antibody','RNA tissue specificity','Reliability (IH)','Reliability (IF)','Subcellular location','RNA tissue specific NX','TPM max in non-specific') + names(header) = c('Gene','description','Evidence','Antibody','RNA tissue category','Reliability (IH)','Reliability (IF)','Subcellular location','RNA TS TPM','TPM max in non-specific') + options = names(header[which(header %in% options)]) + return(options) +} + main = function() { args = get_args() @@ -175,12 +182,16 @@ check_ensembl_geneids(ids) # Read protein atlas - protein_atlas = args$atlas - protein_atlas = read_file(protein_atlas, T) + protein_atlas = read_file(args$atlas, T) # Add expression output = args$output options = strsplit(args$select, ",")[[1]] + if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){ + options = convert_to_previous_header(options) + } else { + options = options[which(options != 'TPM max in non-specific')] + } res = add_expression(ids, protein_atlas, options) # Write output |
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| diff -r 0b279190f90d -r 133309fd6875 add_expression_data.xml --- a/add_expression_data.xml Fri Jun 28 05:01:37 2019 -0400 +++ b/add_expression_data.xml Fri Jan 24 04:22:48 2020 -0500 |
| [ |
| @@ -1,28 +1,41 @@ -<tool id="rna_abbased_data" name="Add expression data" version="2019.06.27"> +<tool id="rna_abbased_data" name="Add expression data" version="2020.01.24"> <description> (RNAseq or Immuno-assays)[Human Protein Atlas] </description> <requirements> - <requirement type="package" version="3.4.1">R</requirement> + <requirement type="package" version="3.4.4">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ - #if $inputtype.filetype == "copy_paste": - - Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output' + Rscript $__tool_directory__/add_expression_HPA.R + --input='$inputtype.genelist' + --select='$options.hpaparams' + --output='$output' + + #if $inputtype.filetype == "copy_paste": + --inputtype="copypaste" + #else + --inputtype="tabfile" + --header='$inputtype.header' + --column='$inputtype.column' + #end if - #else - - Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output' - - #end if - + #if "protein_atlas" in str($ref_file).split("/") + --atlas="$ref_file" + #else + --atlasf="$__tool_directory__/$ref_file" + #end if ]]></command> <inputs> + <param name="ref_file" type="select" label="HPA source file version" > + <options from_data_table="proteore_protein_full_atlas"> + <filter type="sort_by" column="0"/> + </options> + </param> <conditional name="inputtype"> <param name="filetype" type="select" label="Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787)" help="Copy/paste or from a file (e.g. table)"> <option value="file_all" selected="true">Input file containing your IDs</option> @@ -54,12 +67,12 @@ <option value="Gene description" selected="false">Gene description</option> <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> <option value="Antibody">Antibody reference</option> - <option value="RNA tissue category">RNA tissue category</option> - <option value="Reliability (IH)">IH detection level</option> + <option value="RNA tissue specificity">RNA tissue category</option> + <option value="Reliability (IH)">IH detection level</option> <option value="Reliability (IF)">IF detection level</option> <option value="Subcellular location">Subcellular location</option> - <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> - <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> + <option value="RNA tissue specific NX">RNA tissue specificity abundance in 'Transcript Per Million'</option> + <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million' (only for 23/10/2018 release)</option> </param> </section> @@ -124,7 +137,7 @@ - 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. +- RNA non-specific tissue abundance in 'Transcript Per Million' (only available from 23/10/2018 release): please refer to http://www.proteinatlas.org/about/assays+annotation#rna. ----- @@ -134,9 +147,13 @@ ----- -**Data sources (release date)** +**HPA source file version (release date)** + +Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38 -HPA source file (data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38): http://www.proteinatlas.org/download/proteinatlas.tab.gz +Release date 21/01/2020: a subset of the data in the Human Protein Atlas version 19.1 + +downloaded from: http://www.proteinatlas.org/download/proteinatlas.tab.gz ----- |
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| diff -r 0b279190f90d -r 133309fd6875 proteinatlas.csv --- a/proteinatlas.csv Fri Jun 28 05:01:37 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,19629 +0,0 @@\n-Gene\tGene synonym\tEnsembl\tGene description\tChromosome\tPosition\tProtein class\tEvidence\tHPA evidence\tUniProt evidence\tMS evidence\tAntibody\tReliability (IH)\tReliability (Mouse Brain)\tReliability (IF)\tSubcellular location\tRNA tissue category\tRNA TS\tRNA TS TPM\tTPM max in non-specific\n-TSPAN6\tT245, TM4SF6, TSPAN-6\tENSG00000000003\tTetraspanin 6\tX\t100627109-100639991\tPredicted intracellular proteins, Predicted membrane proteins\tEvidence at protein level\tEvidence at transcript level\tEvidence at protein level\tEvidence at protein level\tHPA004109\tApproved\t\tApproved\tCytosol\tMixed\t\t\tfallopian tube: 101.0\n-TNMD\tBRICD4, ChM1L, myodulin, TEM, tendin\tENSG00000000005\tTenomodulin\tX\t100584802-100599885\tPredicted membrane proteins\tEvidence at protein level\tEvidence at transcript level\tEvidence at protein level\t\tHPA034961, HPA055634\tUncertain\t\t\t\tTissue enhanced\t0\tadipose tissue: 10.1;seminal vesicle: 32.9\tbreast: 4.3\n-DPM1\tCDGIE, MPDS\tENSG00000000419\tDolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit\t20\t50934867-50958555\tDisease related genes, Enzymes, Plasma proteins, Potential drug targets, Predicted intracellular proteins\tEvidence at protein level\tEvidence at transcript level\tEvidence at protein level\tEvidence at protein level\tHPA051818\tApproved\t\t\t\tExpressed in all\t\t\tthyroid gland: 80.6\n-SCYL3\tPACE-1, PACE1\tENSG00000000457\tSCY1-like, kinase-like 3\t1\t169849631-169894267\tEnzymes, Predicted intracellular proteins\tEvidence at protein level\tEvidence at transcript level\tEvidence at protein level\tEvidence at protein level\tHPA005624\tApproved\t\tUncertain\tNuclear bodies<br>Microtubules\tExpressed in all\t\t\tparathyroid gland: 44.0\n-C1orf112\tFLJ10706\tENSG00000000460\tChromosome 1 open reading frame 112\t1\t169662007-169854080\tPredicted intracellular proteins\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tHPA023778, HPA024451\tUncertain\t\tApproved\tMitochondria\tTissue enhanced\t0\tparathyroid gland: 24.1;testis: 13.1\tlymph node: 4.1\n-FGR\tc-fgr, p55c-fgr, SRC2\tENSG00000000938\tFGR proto-oncogene, Src family tyrosine kinase\t1\t27612064-27635277\tDisease related genes, Enzymes, Plasma proteins, Potential drug targets, Predicted intracellular proteins\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tHPA002024\tSupported\t\tApproved\tPlasma membrane<br>Aggresome\tTissue enhanced\t0\tappendix: 87.8;bone marrow: 137.2;spleen: 92.1\tlung: 56.3\n-CFH\tARMD4, ARMS1, FHL1, HF, HF1, HF2, HUS\tENSG00000000971\tComplement factor H\t1\t196651878-196747504\tCancer-related genes, Disease related genes, Plasma proteins, Predicted secreted proteins\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tCAB016385, CAB016769, HPA038922, HPA049176, HPA053326\tSupported\t\tApproved\tVesicles\tTissue enhanced\t0\tliver: 838.9\tgallbladder: 206.0\n-FUCA2\tdJ20N2.5, MGC1314\tENSG00000001036\tFucosidase, alpha-L- 2, plasma\t6\t143494811-143511690\tEnzymes, Plasma proteins, Predicted intracellular proteins, Predicted secreted proteins\tEvidence at protein level\tEvidence at transcript level\tEvidence at protein level\tEvidence at protein level\tHPA031659, HPA031660, HPA031661\tUncertain\t\t\t\tExpressed in all\t\t\tparathyroid gland: 152.0\n-GCLC\tGCS, GLCL, GLCLC\tENSG00000001084\tGlutamate-cysteine ligase, catalytic subunit\t6\t53497341-53616970\tDisease related genes, Enzymes, Plasma proteins, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tCAB009569, HPA036359, HPA036360\tApproved\t\tApproved\tNucleus<br>Nucleoli<br>Cytosol\tExpressed in all\t\t\tfallopian tube: 81.9\n-NFYA\tCBF-B, HAP2, NF-YA\tENSG00000001167\tNuclear transcription factor Y, alpha\t6\t41072945-41099976\tPredicted intracellular proteins, Transcription factors\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\tEvidence at protei'..b'isease related genes, Enzymes, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\t\tHPA035437, HPA047590\tApproved\t\tApproved\tNucleus\tMixed\t\t\ttestis: 6.2\n-RP11-96L14.8\t\tENSG00000282872\t\t1\t26164161-26168581\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\t\t\t\t\t\tNot detected\t\t\ttestis: 0.7\n-RP11-49P4.7\t\tENSG00000282881\t\t1\t46532166-46533614\tPredicted membrane proteins\tNo evidence\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\tcerebral cortex: 0.3\n-AKR1C3\t\tENSG00000282883\tAldo-keto reductase family 1, member C3\t10\t5048812-5107503\tPredicted intracellular proteins\tEvidence at protein level\tEvidence at protein level\t\tEvidence at protein level\tHPA068265\t\t\tApproved\tNucleus<br>Nucleoli fibrillar center<br>Endoplasmic reticulum<br>Cytosol\tTissue enhanced\t0\tduodenum: 254.5;gallbladder: 246.9\tsmall intestine: 168.3\n-AL365273.1\t\tENSG00000282889\tEctonucleoside triphosphate diphosphohydrolase 1 \t10\t95844477-95866383\tCD markers, Disease related genes, Enzymes, Potential drug targets, Predicted membrane proteins\tEvidence at protein level\tEvidence at transcript level\tEvidence at protein level\tEvidence at protein level\t\t\t\t\t\tMixed\t\t\tsmooth muscle: 17.8\n-AC123512.3\t\tENSG00000282896\tUncharacterized protein C12orf79 \t12\t91987578-91993403\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\tNo evidence\t\t\t\t\t\t\tTissue enhanced\t0\tlymph node: 3.8\tappendix: 2.1\n-BLOC1S5\tdJ303A1.3, MU, MUTED\tENSG00000282913\tBiogenesis of lysosomal organelles complex-1, subunit 5, muted\t6\t8015810-8064376\tPredicted intracellular proteins\tEvidence at protein level\tEvidence at transcript level\t\tEvidence at protein level\tHPA077525\t\t\tApproved\tVesicles\tTissue enhanced\t0\tbreast: 1.5\tcervix: 1.4\n-CTC-281F24.5\t\tENSG00000282936\t\t17\t6636780-6640316\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\t\t\t\t\t\tMixed\t\t\tcerebral cortex: 1.9\n-RABL6\t\tENSG00000282955\tRAB, member RAS oncogene family-like 6\t9\t136808197-136840522\tPredicted intracellular proteins\tEvidence at protein level\tEvidence at transcript level\t\tEvidence at protein level\tHPA044037, HPA050638\tUncertain\t\tUncertain\tNucleus<br>Centrosome<br>Cytosol\tExpressed in all\t\t\tesophagus: 20.2\n-AL513412.1\t\tENSG00000282960\t\t9\t6720949-7076451\tPredicted intracellular proteins\tEvidence at protein level\tEvidence at transcript level\t\tEvidence at protein level\t\t\t\t\t\tTissue enhanced\t0\tfallopian tube: 1.7\tendometrium: 0.9\n-RP1-34B20.21\t\tENSG00000282988\t\t6\t26195595-26199293\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\tHPA041189\tUncertain\t\t\t\tTissue enhanced\t0\tbone marrow: 2.1\ttestis: 0.7\n-RP11-511P7.5\t\tENSG00000283013\t\t7\t150400702-150412470\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\t\t\t\t\t\tMixed\t\t\tspleen: 8.0\n-CAPS\tCAPS1, MGC126562\tENSG00000283027\tCalcyphosine\t19\t5914407-5915322\tPredicted intracellular proteins\tEvidence at protein level\tEvidence at protein level\tEvidence at protein level\t\tHPA043520\tSupported\t\tSupported\tNucleus<br>Plasma membrane<br>Cytosol\tTissue enriched\t9\tfallopian tube: 68.8\tendometrium: 7.3\n-KLF18\t\tENSG00000283039\tKruppel-like factor 18\t1\t44137821-44141631\tPredicted intracellular proteins\tNo evidence\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\ttestis: 0.3\n-RP11-736N17.11\t\tENSG00000283071\t\t14\t103084210-103090027\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\t\t\t\t\t\tTissue enhanced\t0\ttestis: 1.0\tcerebral cortex: 0.5\n-CTD-2331H12.8\t\tENSG00000283088\t\t19\t52880663-52962768\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\t\t\t\t\t\tMixed\t\t\tparathyroid gland: 7.2\n-RP11-141O19.1\t\tENSG00000283093\t\tX\t51681212-51682831\tPredicted intracellular proteins\tEvidence at transcript level\tEvidence at transcript level\t\t\t\t\t\t\t\tTissue enhanced\t0\ttestis: 3.0\tcerebral cortex: 0.8\n' |
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| diff -r 0b279190f90d -r 133309fd6875 proteore_protein_full_atlas.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_protein_full_atlas.loc.sample Fri Jan 24 04:22:48 2020 -0500 |
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| @@ -0,0 +1,2 @@ +#<id> <release> <name> <tissue> <value> +9979818977 HPA_full_atlas_23-10-2018 HPA Full Protein Atlas 23/10/2018 HPA_full_atlas tool-data/HPA_full_atlas_23-10-2018.tsv |
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| diff -r 0b279190f90d -r 133309fd6875 tool-data/HPA_full_atlas_23-10-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/HPA_full_atlas_23-10-2018.tsv Fri Jan 24 04:22:48 2020 -0500 |
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| b'@@ -0,0 +1,19614 @@\n+Gene\tGene synonym\tEnsembl\tGene description\tChromosome\tPosition\tProtein class\tEvidence\tAntibody\tReliability (IH)\tReliability (Mouse Brain)\tReliability (IF)\tSubcellular location\tPrognostic p-value\tRNA cancer category\tRNA tissue category\tRNA TS\tRNA TS TPM\tTPM max in non-specific\tRNA cell line category\tRNA CS\tRNA CS TPM\n+TSPAN6\tT245, TM4SF6, TSPAN-6\tENSG00000000003\tTetraspanin 6\tX\t100627109-100639991\tPredicted intracellular proteins, Predicted membrane proteins\tEvidence at protein level\tHPA004109\tApproved\t\tApproved\tCytosol\t\tExpressed in all\tMixed\t\t\tfallopian tube: 102.1\tCell line enhanced\t\tNTERA-2: 165.6;RT4: 203.5\n+TNMD\tBRICD4, ChM1L, myodulin, TEM, tendin\tENSG00000000005\tTenomodulin\tX\t100584802-100599885\tPredicted membrane proteins\tEvidence at protein level\tHPA034961, HPA055634\tUncertain\t\t\t\t\tMixed\tTissue enhanced\t\tadipose tissue: 10.1;seminal vesicle: 33.2\tbreast: 4.3\tGroup enriched\t19\tHAP1: 6.2;NTERA-2: 14.2\n+DPM1\tCDGIE, MPDS\tENSG00000000419\tDolichyl-phosphate mannosyltransferase subunit 1, catalytic\t20\t50934867-50958555\tDisease related genes, Enzymes, Plasma proteins, Potential drug targets, Predicted intracellular proteins\tEvidence at protein level\tHPA051818\tApproved\t\t\t\tLiver cancer:1.94e-6 (unfavourable)\tExpressed in all\tExpressed in all\t\t\tthyroid gland: 80.5\tExpressed in all\t\t\n+SCYL3\tPACE-1, PACE1\tENSG00000000457\tSCY1 like pseudokinase 3\t1\t169849631-169894267\tEnzymes, Predicted intracellular proteins\tEvidence at protein level\tHPA005624\tApproved\t\tUncertain\tNuclear bodies<br>Microtubules\tUrothelial cancer:8.85e-4 (favourable)\tExpressed in all\tExpressed in all\t\t\tparathyroid gland: 24.6\tExpressed in all\t\t\n+C1orf112\tFLJ10706\tENSG00000000460\tChromosome 1 open reading frame 112\t1\t169662007-169854080\tPredicted intracellular proteins\tEvidence at protein level\tHPA023778, HPA024451\tUncertain\t\tApproved\tMitochondria\tEndometrial cancer:9.56e-5 (unfavourable)\tExpressed in all\tTissue enhanced\t\tparathyroid gland: 25.0\ttestis: 18.6\tExpressed in all\t\t\n+FGR\tc-fgr, p55c-fgr, SRC2\tENSG00000000938\tFGR proto-oncogene, Src family tyrosine kinase\t1\t27612064-27635277\tDisease related genes, Enzymes, Plasma proteins, Potential drug targets, Predicted intracellular proteins\tEvidence at protein level\tHPA002024\tEnhanced\t\tApproved\tPlasma membrane<br>Aggresome\t\tExpressed in all\tTissue enhanced\t\tappendix: 85.6;bone marrow: 137.0;spleen: 90.6\tlung: 56.3\tCell line enhanced\t\tDaudi: 61.4;HMC-1: 25.8;U-266/70: 116.7\n+CFH\tARMD4, ARMS1, FHL1, HF, HF1, HF2, HUS\tENSG00000000971\tComplement factor H\t1\t196651878-196747504\tCancer-related genes, Disease related genes, Plasma proteins, Predicted secreted proteins\tEvidence at protein level\tCAB016385, CAB016769, HPA038922, HPA049176, HPA053326\tSupported\t\tApproved\tVesicles\tRenal cancer:1.92e-6 (unfavourable)\tTissue enriched\tTissue enhanced\t\tliver: 839.5\tgallbladder: 205.3\tCell line enhanced\t\tHHSteC: 100.0;RT4: 176.9\n+FUCA2\tdJ20N2.5, MGC1314\tENSG00000001036\tFucosidase, alpha-L- 2, plasma\t6\t143494811-143511690\tEnzymes, Plasma proteins, Predicted intracellular proteins, Predicted secreted proteins\tEvidence at protein level\tHPA031659, HPA031660, HPA031661\tUncertain\t\t\t\tLiver cancer:2.70e-9 (unfavourable)\tExpressed in all\tExpressed in all\t\t\tparathyroid gland: 154.2\tMixed\t\t\n+GCLC\tGCS, GLCL, GLCLC\tENSG00000001084\tGlutamate-cysteine ligase catalytic subunit\t6\t53497341-53616970\tDisease related genes, Enzymes, Plasma proteins, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins\tEvidence at protein level\tCAB009569, HPA036359, HPA036360\tApproved\t\tApproved\tNucleus<br>Nucleoli<br>Cytosol\tRenal cancer:3.83e-6 (favourable), Thyroid cancer:8.24e-4 (unfavourable)\tExpressed in all\tExpressed in all\t\t\tfallopian tube: 80.9\tExpressed in all\t\t\n+NFYA\tCBF-B, HAP2, NF-YA\tENSG00000001167\tNuclear transcription factor Y subunit alpha\t6\t41072945-41099976\tPredicted intracellular proteins, Transcription factors\tEvidence at protein level\tCAB009250, HPA050779\tEnhanced\t\tEnhanced\tNucleoplasm\tLiver cancer:8.7'..b'unctions<br>Cytosol\t\t\tMixed\t\t\tappendix: 3.3\tMixed\t\t\n+RP11-434N15.2\t\tENSG00000284299\t\t1\t210858125-211134146\tPredicted membrane proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tNot detected\t\t\tcerebral cortex: 0.6\tCell line enhanced\t\tSH-SY5Y: 1.3\n+SSU72P2\t\tENSG00000284306\tSSU72 pseudogene 2\t11\t4242056-4242640\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\tall non-specific tissues: 0.0\tNot detected\t\t\n+C2orf81\thCG40743, LOC388963\tENSG00000284308\tChromosome 2 open reading frame 81\t2\t74414176-74421591\tPredicted intracellular proteins\tEvidence at protein level\tHPA049564, HPA054835\tEnhanced\t\tApproved\tNucleus<br>Nucleoli fibrillar center\t\t\tTissue enhanced\t\tfallopian tube: 28.5;testis: 23.0\tparathyroid gland: 7.9\tCell line enhanced\t\tSCLC-21H: 20.9;SH-SY5Y: 20.5\n+RP11-432M8.5\t\tENSG00000284356\t\t5\t17597232-17597828\tPredicted intracellular proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tTissue enriched\t12\ttestis: 1.2\tall non-specific tissues: 0.0\tNot detected\t\t\n+RP11-321E2.6\t\tENSG00000284373\tPutative TAF11-like protein ENSP00000332601 \t5\t17498231-17498827\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\ttestis: 0.2\tNot detected\t\t\n+LA16c-312E8.5\t\tENSG00000284395\t\t16\t1431035-1433397\tPredicted intracellular proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tTissue enhanced\t\tprostate: 2.6;stomach: 1.4\tduodenum: 0.7\tCell line enriched\t54\tSCLC-21H: 38.7\n+BTBD8\t\tENSG00000284413\tBTB domain containing 8\t1\t92080305-92147840\tPredicted intracellular proteins\tEvidence at transcript level\tHPA035311, HPA035312\tUncertain\t\tApproved\tNucleoplasm\t\t\tNot detected\t\t\tlung: 0.3\tNot detected\t\t\n+SSU72P7\t\tENSG00000284438\tSSU72 pseudogene 7\t11\t4338660-4339244\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\tall non-specific tissues: 0.0\tNot detected\t\t\n+RP11-321E2.2\t\tENSG00000284439\t\t5\t17518367-17518963\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\tall non-specific tissues: 0.0\tNot detected\t\t\n+RABGEF1\t\tENSG00000284461\tRAB guanine nucleotide exchange factor 1\t7\t66628958-66811459\tPredicted intracellular proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tMixed\t\t\tadrenal gland: 8.8\tMixed\t\t\n+RP11-432M8.2\t\tENSG00000284465\t\t5\t17585162-17585758\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\ttestis: 0.2\tNot detected\t\t\n+AC009477.8\t\tENSG00000284479\t\t2\t131035092-131035262\tPredicted membrane proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tTissue enriched\t8\tadipose tissue: 1.1\tcolon,small intestine: 0.1\tCell line enhanced\t\tHEK 293: 1.4\n+RP11-490B18.9\t\tENSG00000284484\t\t16\t75660227-75677009\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\tskin: 0.1\tNot detected\t\t\n+CTD-2265O21.8\t\tENSG00000284491\t\t19\t12802072-12804303\tPredicted secreted proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\ttestis: 0.6\tNot detected\t\t\n+LYNX1\t\tENSG00000284505\tLy6/neurotoxin 1\t8\t142764334-142778224\tPredicted secreted proteins, Transporters\tEvidence at protein level\t\t\t\t\t\t\t\tTissue enhanced\t\tesophagus: 5.8\tskin: 4.0\tNot detected\t\t\n+RP11-303E16.10\t\tENSG00000284512\t\t16\t81022316-81096284\tPredicted secreted proteins\tEvidence at protein level\tHPA041368\tUncertain\t\tApproved\tVesicles\t\t\tTissue enriched\t7\ttestis: 12.0\tcerebral cortex: 1.6\tMixed\t\t\n+RP11-666A8.13\t\tENSG00000284526\t\t17\t76563710-76570544\tPredicted intracellular proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tMixed\t\t\tskin: 20.6\tMixed\t\t\n+SSU72P3\t\tENSG00000284546\tSSU72 pseudogene 3\t11\t4329865-4330449\tPredicted intracellular proteins\tNo evidence\t\t\t\t\t\t\t\tNot detected\t\t\tall non-specific tissues: 0.0\tNot detected\t\t\n+RP11-321E2.5\t\tENSG00000284552\t\t5\t17486231-17486829\tPredicted intracellular proteins\tEvidence at transcript level\t\t\t\t\t\t\t\tNot detected\t\t\tepididymis: 0.4\tCell line enriched\t12\tU-937: 2.5\n+CTA-150C2.22\t\tENSG00000284554\tDNA dC->dU-editing enzyme APOBEC-3D \t22\t39014363-39033276\tPredicted intracellular proteins\tEvidence at protein level\tHPA055116\tApproved\t\t\t\t\t\tMixed\t\t\tfallopian tube: 3.8\tCell line enhanced\t\tfHDF/TERT166: 2.7;HHSteC: 3.4;HSkMC: 2.1;hTEC/SVTERT24-B: 2.0;Karpas-707: 3.5\n' |
| b |
| diff -r 0b279190f90d -r 133309fd6875 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jan 24 04:22:48 2020 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="proteore_protein_full_atlas" comment_char="#"> + <columns>id, release, name, tissue, value</columns> + <file path="tool-data/proteore_protein_full_atlas.loc" /> + </table> +</tables> \ No newline at end of file |