# HG changeset patch
# User proteore
# Date 1518772508 18000
# Node ID 6788a57c5cb56cfbcff478be576f300c771aba0f
# Parent 472ad7da3d927e72e9dd1f006a7fd62f1b7a2b3a
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/Barplot_output_for_topGO_analysis.png
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diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/Barplot_output_for_topGO_analysis_BP_category.png
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diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/Dotplot_output_for_topGO_analysis.png
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diff -r 472ad7da3d92 -r 6788a57c5cb5 test-data/Dotplot_output_for_topGO_analysis_BP_category.png
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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
@@ -0,0 +1,152 @@
+Protein accession number (UniProt) Protein name Number of peptides (razor + unique) neXtProt_ID UniProt.ID GeneID MIM Ensembl
+P15924 Desmoplakin 69 NX_P15924 DESP_HUMAN 1832 125647; 605676; 607450; 607655; 609638; 612908; 615821 ENSG00000096696
+P02538 Keratin, type II cytoskeletal 6A 53 NX_P02538 K2C6A_HUMAN 3853 148041; 615726 ENSG00000205420
+P02768 Serum albumin 44 NX_P02768 ALBU_HUMAN 213 103600; 615999; 616000 ENSG00000163631
+P08779 Keratin, type I cytoskeletal 16 29 NX_P08779 K1C16_HUMAN 3868 148067; 167200; 613000 ENSG00000186832
+Q02413 Desmoglein-1 24 NX_Q02413 DSG1_HUMAN 1828 125670; 148700; 615508 ENSG00000134760
+P07355 Annexin A2;Putative annexin A2-like protein 22 NX_P07355 ANXA2_HUMAN 302 151740 ENSG00000182718
+P14923 Junction plakoglobin 22 NX_P14923 PLAK_HUMAN 3728 173325; 601214; 611528 ENSG00000173801
+P02788 Lactotransferrin 21 NX_P02788 TRFL_HUMAN 4057 150210 ENSG00000012223
+Q9HC84 Mucin-5B 21 NX_Q9HC84 MUC5B_HUMAN 727897 178500; 600770 ENSG00000117983
+P29508 Serpin B3 20 NX_P29508 SPB3_HUMAN 6317 600517 ENSG00000057149
+P63261 Actin, cytoplasmic 2 19 NX_P63261 ACTG_HUMAN 71 102560; 604717; 614583 ENSG00000184009
+Q8N1N4 Keratin, type II cytoskeletal 78 18 NX_Q8N1N4 K2C78_HUMAN 196374 611159 ENSG00000170423
+Q04695 Keratin, type I cytoskeletal 17 18 NX_Q04695 K1C17_HUMAN 3872 148069; 167210; 184500 ENSG00000128422
+P01876 Ig alpha-1 chain C region 16 NX_P01876 IGHA1_HUMAN NA 146900 ENSG00000211895; ENSG00000282633
+Q01469 Fatty acid-binding protein 5, epidermal 15 NX_Q01469 FABP5_HUMAN 2171 605168 ENSG00000164687
+P31944 Caspase-14 15 NX_P31944 CASPE_HUMAN 23581 605848; 617320 ENSG00000105141
+P01833 Polymeric immunoglobulin receptor 15 NX_P01833 PIGR_HUMAN 5284 173880 ENSG00000162896
+P06733 Alpha-enolase 15 NX_P06733 ENOA_HUMAN 2023 172430 ENSG00000074800
+P25311 Zinc-alpha-2-glycoprotein 15 NX_P25311 ZA2G_HUMAN 563 194460 ENSG00000160862
+Q15149 Plectin 15 NX_Q15149 PLEC_HUMAN 5339 131950; 226670; 601282; 612138; 613723; 616487 ENSG00000178209
+P19013 Keratin, type II cytoskeletal 4 13 NX_P19013 K2C4_HUMAN NA 123940; 193900 ENSG00000170477
+Q6KB66 Keratin, type II cytoskeletal 80 13 NX_Q6KB66 K2C80_HUMAN 144501 611161 ENSG00000167767
+Q08188 Protein-glutamine gamma-glutamyltransferase E 12 NX_Q08188 TGM3_HUMAN 7053 600238; 617251 ENSG00000125780
+P13646 Keratin, type I cytoskeletal 13 11 NX_P13646 K1C13_HUMAN 3860 148065; 615785 ENSG00000171401
+Q86YZ3 Hornerin 11 NX_Q86YZ3 HORN_HUMAN 388697 616293 ENSG00000197915
+P04259 Keratin, type II cytoskeletal 6B 10 NX_P04259 K2C6B_HUMAN 3854 148042; 615728 ENSG00000185479
+P02545 Prelamin-A/C;Lamin-A/C 10 NX_P02545 LMNA_HUMAN 4000 115200; 150330; 151660; 159001; 176670; 181350; 212112; 248370; 275210; 605588; 610140; 613205; 616516 ENSG00000160789
+P04083 Annexin A1 10 NX_P04083 ANXA1_HUMAN 301 151690 ENSG00000135046
+P11021 78 kDa glucose-regulated protein 10 NX_P11021 GRP78_HUMAN 3309 138120 ENSG00000044574
+P02787 Serotransferrin 9 NX_P02787 TRFE_HUMAN 7018 190000; 209300 ENSG00000091513
+P04040 Catalase 9 NX_P04040 CATA_HUMAN 847 115500; 614097 ENSG00000121691
+P31151 Protein S100-A7 9 NX_P31151 S10A7_HUMAN 6278 600353 ENSG00000143556
+P31947 14-3-3 protein sigma 9 NX_P31947 1433S_HUMAN 2810 601290 ENSG00000175793
+Q96P63 Serpin B12 9 NX_Q96P63 SPB12_HUMAN 89777 615662 ENSG00000166634
+P14618 Pyruvate kinase PKM 9 NX_P14618 KPYM_HUMAN 5315 179050 ENSG00000067225
+P60174 Triosephosphate isomerase 9 NX_P60174 TPIS_HUMAN 7167 190450; 615512 ENSG00000111669
+Q06830 Peroxiredoxin-1 9 NX_Q06830 PRDX1_HUMAN 5052 176763 ENSG00000117450
+P01040 Cystatin-A 8 NX_P01040 CYTA_HUMAN 1475 184600; 607936 ENSG00000121552
+P05089 Arginase-1 8 NX_P05089 ARGI1_HUMAN 383 207800; 608313 ENSG00000118520
+P01834 Ig kappa chain C region 8 NX_P01834 IGKC_HUMAN NA 147200; 614102 NA
+P04406 Glyceraldehyde-3-phosphate dehydrogenase 8 NX_P04406 G3P_HUMAN 2597 138400 ENSG00000111640
+P0DMV9 Heat shock 70 kDa protein 1B 8 NX_P0DMV9 HS71B_HUMAN 3303; 3304 140550; 603012 ENSG00000204388; ENSG00000224501; ENSG00000212866; ENSG00000231555; ENSG00000232804
+P13639 Elongation factor 2 8 NX_P13639 EF2_HUMAN 1938 130610; 609306 ENSG00000167658
+P35579 Myosin-9 8 NX_P35579 MYH9_HUMAN 4627 153640; 153650; 155100; 160775; 600208; 603622; 605249 ENSG00000100345
+P68371 Tubulin beta-4B chain 8 NX_P68371 TBB4B_HUMAN 10383 602660 ENSG00000188229
+Q8WVV4 Protein POF1B 8 NX_Q8WVV4 POF1B_HUMAN 79983 300603; 300604 ENSG00000124429
+O75635 Serpin B7 7 NX_O75635 SPB7_HUMAN 8710 603357; 615598 ENSG00000166396
+P01857 Ig gamma-1 chain C region 7 NX_P01857 IGHG1_HUMAN NA 147100; 254500 ENSG00000211896; ENSG00000277633
+P61626 Lysozyme C 7 NX_P61626 LYSC_HUMAN 4069 105200; 153450 ENSG00000090382
+P68363 Tubulin alpha-1B chain 7 NX_P68363 TBA1B_HUMAN 10376 602530 ENSG00000123416
+P01009 Alpha-1-antitrypsin;Short peptide from AAT 6 NX_P01009 A1AT_HUMAN 5265 107400; 613490 ENSG00000197249
+P07900 Heat shock protein HSP 90-alpha 6 NX_P07900 HS90A_HUMAN 3320 140571 ENSG00000080824
+Q9NZH8 Interleukin-36 gamma 6 NX_Q9NZH8 IL36G_HUMAN 56300 605542 ENSG00000136688
+O43707 Alpha-actinin-4;Alpha-actinin-1 6 NX_O43707 ACTN4_HUMAN 81 603278; 604638 ENSG00000130402; ENSG00000282844
+O75223 Gamma-glutamylcyclotransferase 6 NX_O75223 GGCT_HUMAN 79017 137170 ENSG00000006625
+P00338 L-lactate dehydrogenase A chain 6 NX_P00338 LDHA_HUMAN 3939 150000; 612933 ENSG00000134333
+P07339 Cathepsin D 6 NX_P07339 CATD_HUMAN 1509 116840; 610127 ENSG00000117984
+P62987 Ubiquitin-60S ribosomal protein L40 6 NX_P62987 RL40_HUMAN 7311 191321 ENSG00000221983
+P10599 Thioredoxin 6 NX_P10599 THIO_HUMAN 7295 187700 ENSG00000136810
+Q9UGM3 Deleted in malignant brain tumors 1 protein 6 NX_Q9UGM3 DMBT1_HUMAN 1755 137800; 601969 ENSG00000187908
+Q9UI42 Carboxypeptidase A4 6 NX_Q9UI42 CBPA4_HUMAN 51200 607635 ENSG00000128510
+P47929 Galectin-7 5 NX_P47929 LEG7_HUMAN 3963; 653499 600615; 617139 ENSG00000178934; ENSG00000205076; ENSG00000282902; ENSG00000283082
+Q13867 Bleomycin hydrolase 5 NX_Q13867 BLMH_HUMAN 642 602403 ENSG00000108578
+Q6P4A8 Phospholipase B-like 1 5 NX_Q6P4A8 PLBL1_HUMAN 79887 NA ENSG00000121316
+O75369 Filamin-B 5 NX_O75369 FLNB_HUMAN 2317 108720; 108721; 112310; 150250; 272460; 603381 ENSG00000136068
+P00441 Superoxide dismutase [Cu-Zn] 5 NX_P00441 SODC_HUMAN 6647 105400; 147450 ENSG00000142168
+P04792 Heat shock protein beta-1 5 NX_P04792 HSPB1_HUMAN 3315 602195; 606595; 608634 ENSG00000106211
+P11142 Heat shock cognate 71 kDa protein 5 NX_P11142 HSP7C_HUMAN 3312 600816 ENSG00000109971
+P58107 Epiplakin 5 NX_P58107 EPIPL_HUMAN 83481 607553 NA
+P60842 Eukaryotic initiation factor 4A-I 5 NX_P60842 IF4A1_HUMAN 1973 602641 ENSG00000161960
+P62937 Peptidyl-prolyl cis-trans isomerase A 5 NX_P62937 PPIA_HUMAN 5478 123840 ENSG00000196262
+P63104 14-3-3 protein zeta/delta 5 NX_P63104 1433Z_HUMAN 7534 601288 ENSG00000164924
+Q92820 Gamma-glutamyl hydrolase 5 NX_Q92820 GGH_HUMAN 8836 601509 ENSG00000137563
+O75342 Arachidonate 12-lipoxygenase, 12R-type 4 NX_O75342 LX12B_HUMAN 242 242100; 603741 ENSG00000179477
+P09211 Glutathione S-transferase P 4 NX_P09211 GSTP1_HUMAN 2950 134660 ENSG00000084207
+P31025 Lipocalin-1 4 NX_P31025 LCN1_HUMAN 3933 151675 ENSG00000160349
+P48594 Serpin B4 4 NX_P48594 SPB4_HUMAN 6318 600518 ENSG00000206073
+Q14574 Desmocollin-3 4 NX_Q14574 DSC3_HUMAN 1825 600271; 613102 ENSG00000134762
+Q5T750 Skin-specific protein 32 4 NX_Q5T750 XP32_HUMAN 100129271 NA ENSG00000198854
+Q6UWP8 Suprabasin 4 NX_Q6UWP8 SBSN_HUMAN 374897 609969 ENSG00000189001
+O60911 Cathepsin L2 4 NX_O60911 CATL2_HUMAN 1515 603308 ENSG00000136943
+P00558 Phosphoglycerate kinase 1 4 NX_P00558 PGK1_HUMAN 5230 300653; 311800 ENSG00000102144
+P04075 Fructose-bisphosphate aldolase A 4 NX_P04075 ALDOA_HUMAN 226 103850; 611881 ENSG00000149925
+P07384 Calpain-1 catalytic subunit 4 NX_P07384 CAN1_HUMAN 823 114220; 616907 ENSG00000014216
+P0CG05 Ig lambda-2 chain C regions 4 NA NA NA NA NA
+P18206 Vinculin 4 NX_P18206 VINC_HUMAN 7414 193065; 611407; 613255 ENSG00000035403
+P62258 14-3-3 protein epsilon 4 NX_P62258 1433E_HUMAN 7531 605066 ENSG00000108953; ENSG00000274474
+P68871 Hemoglobin subunit beta 4 NX_P68871 HBB_HUMAN 3043 140700; 141900; 603902; 603903; 611162; 613985 ENSG00000244734
+Q9C075 Keratin, type I cytoskeletal 23 4 NX_Q9C075 K1C23_HUMAN 25984 606194 ENSG00000108244; ENSG00000263309
+A8K2U0 Alpha-2-macroglobulin-like protein 1 3 NX_A8K2U0 A2ML1_HUMAN 144568 610627 ENSG00000166535
+P00738 Haptoglobin 3 NX_P00738 HPT_HUMAN 3240 140100; 614081 ENSG00000257017
+P01011 Alpha-1-antichymotrypsin 3 NX_P01011 AACT_HUMAN 12 107280 ENSG00000196136
+P02763 Alpha-1-acid glycoprotein 1 3 NX_P02763 A1AG1_HUMAN 5004 138600 ENSG00000229314
+P18510 Interleukin-1 receptor antagonist protein 3 NX_P18510 IL1RA_HUMAN 3557 147679; 612628; 612852 ENSG00000136689
+P22528 Cornifin-B 3 NX_P22528 SPR1B_HUMAN 6699 182266 ENSG00000169469
+P30740 Leukocyte elastase inhibitor 3 NX_P30740 ILEU_HUMAN 1992 130135 ENSG00000021355
+P80188 Neutrophil gelatinase-associated lipocalin 3 NX_P80188 NGAL_HUMAN 3934 600181 ENSG00000148346
+Q15828 Cystatin-M 3 NX_Q15828 CYTM_HUMAN 1474 601891 ENSG00000175315
+Q9HCY8 Protein S100-A14 3 NX_Q9HCY8 S10AE_HUMAN 57402 607986 ENSG00000189334
+P01623 Ig kappa chain V-III region 3 NA NA NA NA NA
+P01877 Ig alpha-2 chain C region 3 NX_P01877 IGHA2_HUMAN NA 147000 ENSG00000211890
+P06396 Gelsolin 3 NX_P06396 GELS_HUMAN 2934 105120; 137350 ENSG00000148180
+P14735 Insulin-degrading enzyme 3 NX_P14735 IDE_HUMAN 3416 146680 ENSG00000119912
+P20933 N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase 3 NX_P20933 ASPG_HUMAN 175 208400; 613228 ENSG00000038002
+P25788 Proteasome subunit alpha type-3 3 NX_P25788 PSA3_HUMAN 5684 176843; 176845 ENSG00000100567
+P26641 Elongation factor 1-gamma 3 NX_P26641 EF1G_HUMAN 1937 130593 ENSG00000254772
+P36952 Serpin B5 3 NX_P36952 SPB5_HUMAN 5268 154790 ENSG00000206075
+P40926 Malate dehydrogenase, mitochondrial 3 NX_P40926 MDHM_HUMAN 4191 154100; 617339 ENSG00000146701
+Q9Y6R7 IgGFc-binding protein 3 NX_Q9Y6R7 FCGBP_HUMAN 8857 617553 ENSG00000281123
+O95274 Ly6/PLAUR domain-containing protein 3 2 NX_O95274 LYPD3_HUMAN 27076 609484 ENSG00000124466
+P00491 Purine nucleoside phosphorylase 2 NX_P00491 PNPH_HUMAN 4860 164050; 613179 ENSG00000198805
+P04080 Cystatin-B 2 NX_P04080 CYTB_HUMAN 1476 254800; 601145 ENSG00000160213
+P09972 Fructose-bisphosphate aldolase C 2 NX_P09972 ALDOC_HUMAN 230 103870 ENSG00000109107
+P19012 Keratin, type I cytoskeletal 15 2 NX_P19012 K1C15_HUMAN 3866 148030 ENSG00000171346
+P20930 Filaggrin 2 NX_P20930 FILA_HUMAN 2312 135940; 146700; 605803 ENSG00000143631
+Q96FX8 p53 apoptosis effector related to PMP-22 2 NX_Q96FX8 PERP_HUMAN 64065 609301 ENSG00000112378
+Q9UIV8 Serpin B13 2 NX_Q9UIV8 SPB13_HUMAN 5275 604445 ENSG00000197641
+P01625 Ig kappa chain V-IV region Len 2 NA NA NA NA NA
+P01765 Ig heavy chain V-III region TIL 2 NA NA NA NA NA
+P01766 Ig heavy chain V-III region BRO 2 NX_P01766 HV313_HUMAN NA NA ENSG00000211942; ENSG00000282286
+P01860 Ig gamma-3 chain C region 2 NX_P01860 IGHG3_HUMAN NA 147120 NA
+P01871 Ig mu chain C region 2 NX_P01871 IGHM_HUMAN NA 147020; 601495 ENSG00000211899; ENSG00000282657
+P05090 Apolipoprotein D 2 NX_P05090 APOD_HUMAN 347 107740 ENSG00000189058
+P06870 Kallikrein-1 2 NX_P06870 KLK1_HUMAN 3816 147910; 615953 ENSG00000167748
+P07858 Cathepsin B 2 NX_P07858 CATB_HUMAN 1508 116810 ENSG00000164733
+P08865 40S ribosomal protein SA 2 NX_P08865 RSSA_HUMAN 3921 150370; 271400 ENSG00000168028
+P11279 Lysosome-associated membrane glycoprotein 1 2 NX_P11279 LAMP1_HUMAN 3916 153330 ENSG00000185896
+P13473 Lysosome-associated membrane glycoprotein 2 2 NX_P13473 LAMP2_HUMAN 3920 300257; 309060 ENSG00000005893
+P19971 Thymidine phosphorylase 2 NX_P19971 TYPH_HUMAN 1890 131222; 603041 ENSG00000025708
+P23284 Peptidyl-prolyl cis-trans isomerase B 2 NX_P23284 PPIB_HUMAN 5479 123841; 259440 ENSG00000166794
+P23396 40S ribosomal protein S3 2 NX_P23396 RS3_HUMAN 6188 600454 ENSG00000149273
+P25705 ATP synthase subunit alpha, mitochondrial 2 NX_P25705 ATPA_HUMAN 498 164360; 615228; 616045 ENSG00000152234
+P27482 Calmodulin-like protein 3 2 NX_P27482 CALL3_HUMAN 810 114184 ENSG00000178363
+P31949 Protein S100-A11 2 NX_P31949 S10AB_HUMAN 6282 603114 ENSG00000163191
+P40121 Macrophage-capping protein 2 NX_P40121 CAPG_HUMAN 822 153615 ENSG00000042493
+P42357 Histidine ammonia-lyase 2 NX_P42357 HUTH_HUMAN 3034 235800; 609457 ENSG00000084110
+P47756 F-actin-capping protein subunit beta 2 NX_P47756 CAPZB_HUMAN 832 601572 ENSG00000077549
+P48637 Glutathione synthetase 2 NX_P48637 GSHB_HUMAN 2937 231900; 266130; 601002 ENSG00000100983
+P49720 Proteasome subunit beta type-3 2 NX_P49720 PSB3_HUMAN 5691 602176 ENSG00000277791; ENSG00000275903
+P50395 Rab GDP dissociation inhibitor beta 2 NX_P50395 GDIB_HUMAN 2665 600767 ENSG00000057608
+P59998 Actin-related protein 2/3 complex subunit 4 2 NX_P59998 ARPC4_HUMAN 10093 604226 ENSG00000241553
+P61160 Actin-related protein 2 2 NX_P61160 ARP2_HUMAN 10097 604221 ENSG00000138071
+P61916 Epididymal secretory protein E1 2 NX_P61916 NPC2_HUMAN 10577 601015; 607625 ENSG00000119655
+P04745 Alpha-amylase 1 23 NX_P04745 AMY1_HUMAN 276; 277; 278 104700; 104701; 104702 ENSG00000174876; ENSG00000187733; ENSG00000237763
+Q9NZT1 Calmodulin-like protein 5 8 NX_Q9NZT1 CALL5_HUMAN 51806 605183 ENSG00000178372
+P12273 Prolactin-inducible protein 6 NX_P12273 PIP_HUMAN 5304 176720 ENSG00000159763
+Q96DA0 Zymogen granule protein 16 homolog B 5 NX_Q96DA0 ZG16B_HUMAN 124220 NA ENSG00000162078; ENSG00000283056
+P01036 Cystatin-S 5 NX_P01036 CYTS_HUMAN 1472 123857 ENSG00000101441
+Q8TAX7 Mucin-7 2 NX_Q8TAX7 MUC7_HUMAN 4589 158375; 600807 ENSG00000171195
+P01037 Cystatin-SN 2 NX_P01037 CYTN_HUMAN 1469 123855 ENSG00000170373
+P09228 Cystatin-SA 2 NX_P09228 CYTT_HUMAN 1470 123856 ENSG00000170369
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
@@ -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
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
@@ -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
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
@@ -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
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 @@
-
-
-
+
+
+
@@ -138,9 +138,9 @@
-
-
-
+
+
+