| Previous changeset 0:472ad7da3d92 (2017-12-04) Next changeset 2:f62d29616966 (2018-02-27) |
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Commit message:
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty |
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modified:
topGO.xml |
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test-data/Barplot_output_for_topGO_analysis_BP_category.png test-data/Dotplot_output_for_topGO_analysis_BP_category.png test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt test-data/Text_output_for_topGO_analysis_BP_category.tabular |
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removed:
test-data/Barplot_output_for_topGO_analysis.png test-data/Dotplot_output_for_topGO_analysis.png test-data/Text_output_for_topGO_analysis.txt test-data/prot_reactome_EGFR_mapped_ensg.txt |
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| diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt Fri Feb 16 04:15:08 2018 -0500 |
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| 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' |
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| diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/Text_output_for_topGO_analysis.txt --- a/test-data/Text_output_for_topGO_analysis.txt Mon Dec 04 09:39:21 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,71 +0,0 @@ -GO.ID Term Annotated Significant Expected pvalues qvalues -GO:0045087 innate immune response 1428 35 2.84 6.5e-27 9.28915e-24 -GO:0007268 synaptic transmission 766 20 1.52 7.2e-17 9.35410909090909e-14 -GO:0019933 cAMP-mediated signaling 56 9 0.11 1.2e-15 1.4291e-12 -GO:0050796 regulation of insulin secretion 208 13 0.41 2.6e-15 2.8582e-12 -GO:0007193 adenylate cyclase-inhibiting G-protein c... 75 9 0.15 1.9e-14 1.93949285714286e-11 -GO:1904322 cellular response to forskolin 5 5 0.01 2.3e-14 2.19128666666667e-11 -GO:0007189 adenylate cyclase-activating G-protein c... 84 9 0.17 5.5e-14 4.91253125e-11 -GO:0002223 stimulatory C-type lectin receptor signa... 139 10 0.28 1.1e-13 9.24711764705882e-11 -GO:0006171 cAMP biosynthetic process 139 13 0.28 1.2e-13 9.52733333333333e-11 -GO:0055085 transmembrane transport 1435 25 2.86 3.7e-13 2.78298421052632e-10 -GO:0007596 blood coagulation 590 21 1.17 9.7e-12 6.931135e-09 -GO:0048010 vascular endothelial growth factor recep... 317 11 0.63 1.6e-11 1.0888380952381e-08 -GO:0038095 Fc-epsilon receptor signaling pathway 316 10 0.63 3.9e-10 2.53340454545455e-07 -GO:0030168 platelet activation 263 11 0.52 6.2e-10 3.85235652173913e-07 -GO:2000480 negative regulation of cAMP-dependent pr... 8 4 0.02 9.2e-10 5.47821666666667e-07 -GO:0038096 Fc-gamma receptor signaling pathway invo... 74 6 0.15 6.7e-09 3.829988e-06 -GO:0010881 regulation of cardiac muscle contraction... 19 4 0.04 5.0e-08 2.74826923076923e-05 -GO:0051343 positive regulation of cyclic-nucleotide... 5 3 0.01 7.2e-08 3.81093333333333e-05 -GO:0010800 positive regulation of peptidyl-threonin... 26 4 0.05 1.9e-07 9.69746428571429e-05 -GO:1901841 regulation of high voltage-gated calcium... 8 3 0.02 4.0e-07 0.00019711724137931 -GO:0022400 regulation of rhodopsin mediated signali... 33 4 0.07 5.2e-07 0.00023972 -GO:0001975 response to amphetamine 33 4 0.07 5.2e-07 0.00023972 -GO:0060316 positive regulation of ryanodine-sensiti... 9 3 0.02 6.0e-07 0.000259836363636364 -GO:1901844 regulation of cell communication by elec... 9 3 0.02 6.0e-07 0.000259836363636364 -GO:0007190 activation of adenylate cyclase activity 35 4 0.07 6.6e-07 0.000277413529411765 -GO:0071361 cellular response to ethanol 11 3 0.02 1.2e-06 0.000476366666666667 -GO:0060315 negative regulation of ryanodine-sensiti... 11 3 0.02 1.2e-06 0.000476366666666667 -GO:0032465 regulation of cytokinesis 98 5 0.2 1.4e-06 0.00054074054054054 -GO:0010801 negative regulation of peptidyl-threonin... 13 3 0.03 2.0e-06 0.000752157894736842 -GO:0007611 learning or memory 229 11 0.46 2.1e-06 0.000769515384615385 -GO:0032516 positive regulation of phosphoprotein ph... 15 3 0.03 3.2e-06 0.00111539512195122 -GO:0005513 detection of calcium ion 15 3 0.03 3.2e-06 0.00111539512195122 -GO:0097338 response to clozapine 2 2 0 3.9e-06 0.00132702142857143 -GO:0051447 negative regulation of meiotic cell cycl... 19 3 0.04 6.9e-06 0.00229320697674419 -GO:0031954 positive regulation of protein autophosp... 20 3 0.04 8.1e-06 0.00263084318181818 -GO:0051000 positive regulation of nitric-oxide synt... 21 3 0.04 9.4e-06 0.00298523111111111 -GO:0000186 activation of MAPKK activity 258 6 0.51 1.1e-05 0.00341741304347826 -GO:0043647 inositol phosphate metabolic process 71 4 0.14 1.2e-05 0.00364876595744681 -GO:0051412 response to corticosterone 26 3 0.05 1.8e-05 0.00524975510204082 -GO:0007616 long-term memory 26 3 0.05 1.8e-05 0.00524975510204082 -GO:0005980 glycogen catabolic process 27 3 0.05 2.0e-05 0.0057164 -GO:0002576 platelet degranulation 89 4 0.18 2.9e-05 0.00812625490196078 -GO:0002027 regulation of heart rate 90 4 0.18 3.0e-05 0.00824480769230769 -GO:0046209 nitric oxide metabolic process 94 4 0.19 3.5e-05 0.00943745283018868 -GO:0046777 protein autophosphorylation 231 8 0.46 3.8e-05 0.0100566296296296 -GO:0035556 intracellular signal transduction 2849 30 5.67 4.1e-05 0.0106532909090909 -GO:0018107 peptidyl-threonine phosphorylation 78 8 0.16 4.3e-05 0.0109734464285714 -GO:0019433 triglyceride catabolic process 35 3 0.07 4.5e-05 0.0112823684210526 -GO:0048016 inositol phosphate-mediated signaling 36 3 0.07 4.9e-05 0.0120734310344828 -GO:1901621 negative regulation of smoothened signal... 6 2 0.01 5.7e-05 0.0138065593220339 -GO:0050730 regulation of peptidyl-tyrosine phosphor... 214 5 0.43 6.2e-05 0.0147673666666667 -GO:0042045 epithelial fluid transport 7 2 0.01 8.0e-05 0.0187422950819672 -GO:0044281 small molecule metabolic process 2690 28 5.35 8.4e-05 0.019362 -GO:0018105 peptidyl-serine phosphorylation 237 5 0.47 0.00010 0.022684126984127 -GO:0021762 substantia nigra development 47 3 0.09 0.00011 0.02456265625 -GO:0034351 negative regulation of glial cell apopto... 9 2 0.02 0.00014 0.0307806153846154 -GO:0007411 axon guidance 600 7 1.19 0.00015 0.0324795454545454 -GO:0090330 regulation of platelet aggregation 13 2 0.03 0.00030 0.063989552238806 -GO:0008286 insulin receptor signaling pathway 361 7 0.72 0.00036 0.0745617391304348 -GO:0070588 calcium ion transmembrane transport 205 7 0.41 0.00036 0.0745617391304348 -GO:0071902 positive regulation of protein serine/th... 316 5 0.63 0.00038 0.0775797142857143 -GO:0046827 positive regulation of protein export fr... 15 2 0.03 0.00040 0.080512676056338 -GO:0071380 cellular response to prostaglandin E sti... 17 2 0.03 0.00051 0.0998412328767123 -GO:0035413 positive regulation of catenin import in... 17 2 0.03 0.00051 0.0998412328767123 -GO:0045787 positive regulation of cell cycle 340 5 0.68 0.00053 0.102354459459459 -GO:0006094 gluconeogenesis 84 3 0.17 0.00062 0.118138933333333 -GO:0051592 response to calcium ion 114 6 0.23 0.00077 0.144790394736842 -GO:0043536 positive regulation of blood vessel endo... 22 2 0.04 0.00087 0.16146974025974 -GO:0071364 cellular response to epidermal growth fa... 23 2 0.05 0.00095 0.174057051282051 -GO:0042752 regulation of circadian rhythm 98 3 0.2 0.00097 0.175471772151899 |
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| diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/Text_output_for_topGO_analysis_BP_category.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Text_output_for_topGO_analysis_BP_category.tabular Fri Feb 16 04:15:08 2018 -0500 |
| b |
| @@ -0,0 +1,36 @@ +GO.ID Term Annotated Significant Expected pvalues qvalues +GO:0070268 cornification 125 19 0.85 1.3e-20 1.007175e-16 +GO:0001895 retina homeostasis 72 13 0.49 1.9e-15 9.8135e-12 +GO:0010951 negative regulation of endopeptidase act... 253 19 1.72 8.7e-15 3.3701625e-11 +GO:0061621 canonical glycolysis 28 7 0.19 6.1e-10 1.89039e-06 +GO:0018149 peptide cross-linking 60 7 0.41 1.7e-07 0.000420578571428571 +GO:0061436 establishment of skin barrier 20 5 0.14 1.9e-07 0.000420578571428571 +GO:0042542 response to hydrogen peroxide 127 11 0.87 4.1e-07 0.00079411875 +GO:0002576 platelet degranulation 142 9 0.97 5.6e-07 0.000964133333333333 +GO:0098869 cellular oxidant detoxification 112 8 0.76 9.8e-07 0.00151851 +GO:0006094 gluconeogenesis 82 7 0.56 1.4e-06 0.00197209090909091 +GO:0001580 detection of chemical stimulus involved ... 55 6 0.37 2.0e-06 0.0025825 +GO:0007568 aging 297 11 2.02 6.1e-06 0.00727073076923077 +GO:0042744 hydrogen peroxide catabolic process 23 4 0.16 1.6e-05 0.017561 +GO:0045104 intermediate filament cytoskeleton organ... 47 5 0.32 1.7e-05 0.017561 +GO:0002934 desmosome organization 10 3 0.07 3.6e-05 0.03486375 +GO:0042493 response to drug 434 12 2.96 4.2e-05 0.0375142105263158 +GO:0045471 response to ethanol 138 7 0.94 4.5e-05 0.0375142105263158 +GO:0061740 protein targeting to lysosome involved i... 2 2 0.01 4.6e-05 0.0375142105263158 +GO:0070527 platelet aggregation 61 5 0.42 6.0e-05 0.046485 +GO:0046686 response to cadmium ion 64 5 0.44 7.5e-05 0.0553392857142857 +GO:0046718 viral entry into host cell 154 7 1.05 9.0e-05 0.0633886363636364 +GO:0043163 cell envelope organization 3 2 0.02 0.00014 0.0943173913043478 +GO:0070301 cellular response to hydrogen peroxide 83 5 0.57 0.00026 0.166869230769231 +GO:1903923 positive regulation of protein processin... 4 2 0.03 0.00027 0.166869230769231 +GO:0046716 muscle cell cellular homeostasis 19 3 0.13 0.00028 0.166869230769231 +GO:0051016 barbed-end actin filament capping 21 3 0.14 0.00038 0.218077777777778 +GO:0033591 response to L-ascorbic acid 5 2 0.03 0.00045 0.249026785714286 +GO:0019730 antimicrobial humoral response 95 5 0.65 0.00048 0.256468965517241 +GO:0006953 acute-phase response 56 4 0.38 0.00057 0.294405 +GO:0086073 bundle of His cell-Purkinje myocyte adhe... 6 2 0.04 0.00068 0.32926875 +GO:0071638 negative regulation of monocyte chemotac... 6 2 0.04 0.00068 0.32926875 +GO:0031069 hair follicle morphogenesis 27 3 0.18 0.00080 0.375636363636364 +GO:0048102 autophagic cell death 7 2 0.05 0.00095 0.408895833333333 +GO:0009635 response to herbicide 7 2 0.05 0.00095 0.408895833333333 +GO:0044829 positive regulation by host of viral gen... 7 2 0.05 0.00095 0.408895833333333 |
| b |
| diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/prot_reactome_EGFR_mapped_ensg.txt --- a/test-data/prot_reactome_EGFR_mapped_ensg.txt Mon Dec 04 09:39:21 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,36 +0,0 @@ -ENSG00000005249 -ENSG00000072062 -ENSG00000078295 -ENSG00000096433 -ENSG00000108946 -ENSG00000114302 -ENSG00000115252 -ENSG00000118260 -ENSG00000121281 -ENSG00000123104 -ENSG00000123360 -ENSG00000124181 -ENSG00000126583 -ENSG00000129467 -ENSG00000138031 -ENSG00000138798 -ENSG00000142875 -ENSG00000143933 -ENSG00000146648 -ENSG00000150995 -ENSG00000152495 -ENSG00000154229 -ENSG00000154678 -ENSG00000155897 -ENSG00000160014 -ENSG00000162104 -ENSG00000163932 -ENSG00000164742 -ENSG00000165059 -ENSG00000168710 -ENSG00000171132 -ENSG00000173020 -ENSG00000173175 -ENSG00000174233 -ENSG00000188191 -ENSG00000198668 |
| b |
| diff -r 472ad7da3d92 -r 6788a57c5cb5 topGO.xml --- a/topGO.xml Mon Dec 04 09:39:21 2017 -0500 +++ b/topGO.xml Fri Feb 16 04:15:08 2018 -0500 |
| [ |
| @@ -120,9 +120,9 @@ <test> <conditional name="inputtype"> <param name="filetype " value="tabfile"/> - <param name="genelist" value="prot_reactome_EGFR_mapped_ensg.txt"/> - <param name="column" value="c1"/> - <param name="header" value="FALSE"/> + <param name="genelist" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/> + <param name="column" value="c8"/> + <param name="header" value="TRUE"/> </conditional> <param name="ontocat" value="BP"/> <param name="option" value="elim"/> @@ -138,9 +138,9 @@ <param name="dotoutput" value="TRUE"/> </conditional> <param name="geneuniverse" value="org.Hs.eg.db"/> - <output name="outputtext" file="Text_output_for_topGO_analysis.txt"/> - <output name="outputbarplot" file="Barplot_output_for_topGO_analysis.png"/> - <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis.png"/> + <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/> + <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/> + <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/> </test> </tests> <help><
