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changeset 1:6788a57c5cb5 draft

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planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author proteore
date Fri, 16 Feb 2018 04:15:08 -0500
parents 472ad7da3d92
children f62d29616966
files test-data/Barplot_output_for_topGO_analysis.png test-data/Barplot_output_for_topGO_analysis_BP_category.png test-data/Dotplot_output_for_topGO_analysis.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.txt test-data/Text_output_for_topGO_analysis_BP_category.tabular test-data/prot_reactome_EGFR_mapped_ensg.txt topGO.xml
diffstat 9 files changed, 194 insertions(+), 113 deletions(-) [+]
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Binary file test-data/Barplot_output_for_topGO_analysis.png has changed
Binary file test-data/Barplot_output_for_topGO_analysis_BP_category.png has changed
Binary file test-data/Dotplot_output_for_topGO_analysis.png has changed
Binary file test-data/Dotplot_output_for_topGO_analysis_BP_category.png has changed
--- /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
--- 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
--- /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
--- 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
--- 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><![CDATA[