# command: ../../../transit/src/transit.py pathway_enrichment resampling_glyc_chol.txt /pacific/home/ioerger/transit/src/pytransit/analysis/H37Rv_sanger_roles.dat /pacific/home/ioerger/transit/src/pytransit/analysis/sanger_roles.dat pathways_glyc_chol_Sanger.txt
# date: 2020-02-29 09:21:58.928719
# method=FISHER, PC=2
# genes with associations=3906 out of 3990 total
# significant genes (qval<0.05): 75
# 118 out of 123 pathways have >=1 gene; max has 1066
#pathway	total_genes(M)	genes_in_path(n)	significant_genes(N)	signif_genes_in_path(k)	expected	k+PC	n_adj_by_PC	enrichement	pval	qval	description	genes
I	3990	1066	75	37	20.04	39	1172	1.77	9.991730975992556e-06	0.0011790242551671217	Small-molecule metabolism	Rv0244c/fadE5 Rv0391/metZ Rv0485/- Rv0693/pqqE Rv0694/lldD1 Rv0761c/adhB Rv1129c/- Rv1131/gltA1 Rv1193/fadD36 Rv1432/- Rv1626/- Rv1627c/- Rv1963c/mce3R Rv2048c/pks12 Rv2506/- Rv3502c/fabG Rv3526/- Rv3535c/- Rv3537/- Rv3543c/fadE29 Rv3544c/fadE28 Rv3546/fadA5 Rv3549c/- Rv3551/- Rv3553/- Rv3556c/fadA6 Rv3559c/- Rv3560c/fadE30 Rv3561/fadD3 Rv3563/fadE32 Rv3564/fadE33 Rv3568c/bphC Rv3570c/- Rv3571/hmp Rv3575c/- Rv3696c/glpK Rv3825c/pks2
I.A	3990	163	75	12	3.06	14	269	2.767	0.00010506620369689351	0.005761441690236816	Degradation	Rv0244c/fadE5 Rv1193/fadD36 Rv3543c/fadE29 Rv3544c/fadE28 Rv3546/fadA5 Rv3551/- Rv3556c/fadA6 Rv3560c/fadE30 Rv3561/fadD3 Rv3563/fadE32 Rv3564/fadE33 Rv3696c/glpK
I.B.7	3990	171	75	12	3.21	14	277	2.687	0.00014647733110771565	0.005761441690236816	Miscellaneous oxidoreductases and oxygenases	Rv0761c/adhB Rv1432/- Rv3502c/fabG Rv3526/- Rv3535c/- Rv3537/- Rv3549c/- Rv3553/- Rv3559c/- Rv3568c/bphC Rv3570c/- Rv3571/hmp
I.A.3	3990	119	75	10	2.24	12	225	2.83	0.00022884333790751995	0.006750878468271839	Fatty acids	Rv0244c/fadE5 Rv1193/fadD36 Rv3543c/fadE29 Rv3544c/fadE28 Rv3546/fadA5 Rv3556c/fadA6 Rv3560c/fadE30 Rv3561/fadD3 Rv3563/fadE32 Rv3564/fadE33
IV.A	3990	38	75	7	0.71	9	144	3.321	0.0003039914374397945	0.00717419792357915	Virulence	Rv3494c/mce4F Rv3496c/mce4D Rv3497c/mce4C Rv3498c/mce4B Rv3499c/mce4A Rv3500c/yrbE4B Rv3501c/yrbE4A
I.B	3990	292	75	14	5.49	16	398	2.136	0.0008651960541267495	0.017015522397826072	Energy Metabolism	Rv0694/lldD1 Rv0761c/adhB Rv1131/gltA1 Rv1432/- Rv3502c/fabG Rv3526/- Rv3535c/- Rv3537/- Rv3549c/- Rv3553/- Rv3559c/- Rv3568c/bphC Rv3570c/- Rv3571/hmp
III.A	3990	123	75	6	2.31	8	229	1.856	0.026401103269226858	0.3986985138483363	Transport/binding proteins	Rv0362/mgtE Rv1283c/oppB Rv2684/arsA Rv2936/drrA Rv2938/drrC Rv3540c/ltp2
II.C.4	3990	17	75	3	0.32	5	123	2.155	0.027030407718531275	0.3986985138483363	Conserved membrane proteins	Rv0450c/mmpL4 Rv1183/mmpL10 Rv2942/mmpL7
III	3990	206	75	7	3.87	9	312	1.533	0.06492068467711051	0.5627078488075394	Cell Processes	Rv0362/mgtE Rv1283c/oppB Rv2462c/tig Rv2684/arsA Rv2936/drrA Rv2938/drrC Rv3540c/ltp2
III.A.6	3990	20	75	2	0.38	4	126	1.681	0.08680065818505082	0.5627078488075394	Efflux proteins	Rv2936/drrA Rv2938/drrC
I.J.1	3990	143	75	5	2.69	7	249	1.493	0.09337686799842691	0.5627078488075394	Repressors/activators	Rv0485/- Rv1129c/- Rv1963c/mce3R Rv2506/- Rv3575c/-
I.J	3990	187	75	6	3.52	8	293	1.449	0.09610795443903061	0.5627078488075394	Broad regulatory functions	Rv0485/- Rv1129c/- Rv1626/- Rv1963c/mce3R Rv2506/- Rv3575c/-
I.I	3990	41	75	2	0.77	4	147	1.444	0.14116711810808064	0.5627078488075394	Polyketide and non-ribosomal peptide synthesis	Rv2048c/pks12 Rv3825c/pks2
III.A.5	3990	2	75	1	0.04	3	108	1.471	0.14413240540199004	0.5627078488075394	Fatty acid transport	Rv3540c/ltp2
III.D	3990	14	75	1	0.26	3	120	1.327	0.18788653746430714	0.5627078488075394	Protein and peptide secretion	Rv2462c/tig
I.G.11	3990	15	75	1	0.28	3	121	1.316	0.19171693528204453	0.5627078488075394	Menaquinone, PQQ, ubiquinone and other terpenoids	Rv0693/pqqE
III.A.1	3990	17	75	1	0.32	3	123	1.293	0.19945298362323038	0.5627078488075394	Amino acids	Rv1283c/oppB
I.A.2	3990	18	75	1	0.34	3	124	1.282	0.2033573123217084	0.5627078488075394	Amino acids and amines	Rv3551/-
IV.I	3990	18	75	1	0.34	3	124	1.282	0.2033573123217084	0.5627078488075394	Miscellaneous phosphatases, lyases, and hydrolases	Rv3569c/bphD
I.B.3	3990	19	75	1	0.36	3	125	1.271	0.20728496086029607	0.5627078488075394	TCA cycle	Rv1131/gltA1
I.D.2	3990	21	75	1	0.39	3	127	1.255	0.21520756355543375	0.5627078488075394	Aspartate family	Rv0391/metZ
II.C.1	3990	65	75	2	1.22	4	171	1.242	0.2173611100419728	0.5627078488075394	Lipoproteins(lppA-lpr0)	Rv2945c/lppX Rv3495c/lprN
I.A.1	3990	22	75	1	0.41	3	128	1.245	0.219201190042899	0.5627078488075394	Carbon compounds	Rv3696c/glpK
IV.F	3990	22	75	1	0.41	3	128	1.245	0.219201190042899	0.5627078488075394	Cytochrome P450 enzymes	Rv3545c/cyp125
I.H.3	3990	25	75	1	0.47	3	131	1.215	0.23130340806825936	0.5627078488075394	Acyltransferases, Mycoloyltransferases, and phospholipid synthesis	Rv1627c/-
I.B.6.a	3990	30	75	1	0.56	3	136	1.172	0.2518385673959124	0.5627078488075394	aerobic	Rv0694/lldD1
I.J.2	3990	30	75	1	0.56	3	136	1.172	0.2518385673959124	0.5627078488075394	Two component systems	Rv1626/-
III.A.2	3990	31	75	1	0.58	3	137	1.163	0.2559944028458324	0.5627078488075394	Cations	Rv0362/mgtE
III.A.4	3990	34	75	1	0.64	3	140	1.136	0.26854780150698676	0.5627078488075394	Anions	Rv2684/arsA
IV	3990	469	75	10	8.82	12	575	1.109	0.27851729288325916	0.5627078488075394	Other	Rv3135/PPE50 Rv3494c/mce4F Rv3496c/mce4D Rv3497c/mce4C Rv3498c/mce4B Rv3499c/mce4A Rv3500c/yrbE4B Rv3501c/yrbE4A Rv3545c/cyp125 Rv3569c/bphD
II.C.2	3990	39	75	1	0.73	3	145	1.099	0.2897180072081357	0.5627078488075394	Surface polysaccharides, lipopolysaccharides, proteins and antigens	Rv0806c/cpsY
I.C.2	3990	2	75	0	0.04	2	108	0.98	0.33155934374819307	0.5627078488075394	Gluconeogenesis	
I.G.3	3990	2	75	0	0.04	2	108	0.98	0.33155934374819307	0.5627078488075394	Lipoate	
IV.K	3990	2	75	0	0.04	2	108	0.98	0.33155934374819307	0.5627078488075394	Chelatases	
II.A.2	3990	3	75	0	0.06	2	109	0.971	0.33676549576446313	0.5627078488075394	Ribosome modification and maturation	
II.B.2	3990	3	75	0	0.06	2	109	0.971	0.33676549576446313	0.5627078488075394	DNA	
IV.E	3990	3	75	0	0.06	2	109	0.971	0.33676549576446313	0.5627078488075394	Bacteriocin-like proteins	
IV.G	3990	3	75	0	0.06	2	109	0.971	0.33676549576446313	0.5627078488075394	Coenzyme F420-dependent enzymes	
I.A.4	3990	4	75	0	0.08	2	110	0.962	0.3419705696065737	0.5627078488075394	Phosphorous compounds	
I.G.5	3990	4	75	0	0.08	2	110	0.962	0.3419705696065737	0.5627078488075394	Pantothenate	
I.G.7	3990	4	75	0	0.08	2	110	0.962	0.3419705696065737	0.5627078488075394	Pyridine nucleotide	
I.G.8	3990	4	75	0	0.08	2	110	0.962	0.3419705696065737	0.5627078488075394	Thiamine	
II.A.4	3990	4	75	0	0.08	2	110	0.962	0.3419705696065737	0.5627078488075394	Nucleoproteins	
I.B.4	3990	5	75	0	0.09	2	111	0.957	0.34717365602264	0.5627078488075394	Glyoxylate bypass	
I.B.2	3990	6	75	0	0.11	2	112	0.948	0.3523738628495694	0.5627078488075394	Pyruvate dehydrogenase	
I.G.14	3990	6	75	0	0.11	2	112	0.948	0.3523738628495694	0.5627078488075394	Iron utilisation	
II.B.1	3990	6	75	0	0.11	2	112	0.948	0.3523738628495694	0.5627078488075394	RNA	
IV.B.1.b	3990	6	75	0	0.11	2	112	0.948	0.3523738628495694	0.5627078488075394	IS1081	
IV.J	3990	6	75	0	0.11	2	112	0.948	0.3523738628495694	0.5627078488075394	Cyclases	
I.B.8	3990	8	75	0	0.15	2	114	0.93	0.362762154519012	0.5627078488075394	ATP-proton motive force	
I.G.1	3990	8	75	0	0.15	2	114	0.93	0.362762154519012	0.5627078488075394	Biotin	
I.G.10	3990	8	75	0	0.15	2	114	0.93	0.362762154519012	0.5627078488075394	Thioredoxin, glutaredoxin and mycothiol	
I.G.9	3990	8	75	0	0.15	2	114	0.93	0.362762154519012	0.5627078488075394	Riboflavin	
II.A.8	3990	8	75	0	0.15	2	114	0.93	0.362762154519012	0.5627078488075394	Polysaccharides (cytoplasmic)	
II.B.4	3990	8	75	0	0.15	2	114	0.93	0.362762154519012	0.5627078488075394	Polysaccharides, lipopolysaccharides and phospholipids	
I.F.2	3990	9	75	0	0.17	2	115	0.922	0.36794854041165803	0.5627078488075394	Pyrimidine ribonucleotide biosynthesis	
I.F.5	3990	9	75	0	0.17	2	115	0.922	0.36794854041165803	0.5627078488075394	Miscellaneous nucleoside/nucleotide reactions	
I.G.12	3990	9	75	0	0.17	2	115	0.922	0.36794854041165803	0.5627078488075394	Heme and porphyrin	
II.B.6	3990	9	75	0	0.17	2	115	0.922	0.36794854041165803	0.5627078488075394	Aromatic hydrocarbons	
I.F.4	3990	10	75	0	0.19	2	116	0.913	0.373128648746379	0.5627078488075394	Salvage of nucleosides and nucleotides	
IV.B.2	3990	10	75	0	0.19	2	116	0.913	0.373128648746379	0.5627078488075394	REP13E12 family	
II.C	3990	360	75	7	6.77	9	466	1.026	0.37824916635444594	0.5627078488075394	Cell envelope	Rv0450c/mmpL4 Rv0806c/cpsY Rv1183/mmpL10 Rv2942/mmpL7 Rv2945c/lppX Rv3200c/- Rv3495c/lprN
I.B.5	3990	11	75	0	0.21	2	117	0.905	0.37830167254783503	0.5627078488075394	Pentose phosphate pathway	
I.D.5	3990	11	75	0	0.21	2	117	0.905	0.37830167254783503	0.5627078488075394	Histidine	
I.G.2	3990	11	75	0	0.21	2	117	0.905	0.37830167254783503	0.5627078488075394	Folic acid	
I.B.6	3990	60	75	1	1.13	3	166	0.958	0.380409629225454	0.5627078488075394	Respiration	Rv0694/lldD1
I.B.1	3990	12	75	0	0.23	2	118	0.897	0.3834668217413584	0.5627078488075394	Glycolysis	
III.E	3990	12	75	0	0.23	2	118	0.897	0.3834668217413584	0.5627078488075394	Adaptations and atypical conditions	
I.C.1	3990	13	75	0	0.24	2	119	0.893	0.3886233231032874	0.5627078488075394	General	
I.D.7	3990	13	75	0	0.24	2	119	0.893	0.3886233231032874	0.5627078488075394	Branched amino acid family	
I.C.3	3990	14	75	0	0.26	2	120	0.885	0.39377042016777336	0.5627078488075394	Sugar nucleotides	
I.H.2	3990	14	75	0	0.26	2	120	0.885	0.39377042016777336	0.5627078488075394	Modification of fatty and mycolic acids	
I.J.3	3990	14	75	0	0.26	2	120	0.885	0.39377042016777336	0.5627078488075394	Serine-Threonine protein kinases and phosphoprotein phosphatases	
IV.D	3990	14	75	0	0.26	2	120	0.885	0.39377042016777336	0.5627078488075394	Antibiotic production and resistance	
I.B.6.b	3990	15	75	0	0.28	2	121	0.877	0.39890737317369557	0.5627078488075394	anaerobic	
I.B.6.c	3990	15	75	0	0.28	2	121	0.877	0.39890737317369557	0.5627078488075394	Electron transport	
I.C.5	3990	15	75	0	0.28	2	121	0.877	0.39890737317369557	0.5627078488075394	Sulphur metabolism	
I.D.3	3990	15	75	0	0.28	2	121	0.877	0.39890737317369557	0.5627078488075394	Serine family	
I.D.4	3990	15	75	0	0.28	2	121	0.877	0.39890737317369557	0.5627078488075394	Aromatic amino acid family	
II.A.6	3990	15	75	0	0.28	2	121	0.877	0.39890737317369557	0.5627078488075394	Protein translation and modification	
I.H	3990	65	75	1	1.22	3	171	0.932	0.402046838484083	0.5627078488075394	Lipid Biosynthesis	Rv1627c/-
III.B	3990	16	75	0	0.3	2	122	0.87	0.4040334589529203	0.5627078488075394	Chaperones/Heat shock	
I.G.13	3990	17	75	0	0.32	2	123	0.862	0.40914797083600124	0.5627078488075394	Cobalamin	
IV.C.2	3990	68	75	1	1.28	3	174	0.915	0.41497775723520786	0.5627078488075394	PPE family	Rv3135/PPE50
I.D.1	3990	19	75	0	0.36	2	125	0.847	0.4193395281823238	0.5627078488075394	Glutamate family	
III.A.3	3990	19	75	0	0.36	2	125	0.847	0.4193395281823238	0.5627078488075394	Carbohydrates, organic acids and alcohols	
III.C	3990	19	75	0	0.36	2	125	0.847	0.4193395281823238	0.5627078488075394	Cell division	
I.F.1	3990	20	75	0	0.38	2	126	0.84	0.42441524189721197	0.5627078488075394	Purine ribonucleotide biosynthesis	
I.G.4	3990	20	75	0	0.38	2	126	0.84	0.42441524189721197	0.5627078488075394	Molybdopterin	
III.F	3990	22	75	0	0.41	2	128	0.83	0.43452333065778487	0.5697083668624291	Detoxification	
I.H.1	3990	26	75	0	0.49	2	132	0.803	0.45454918150765466	0.5830087328032961	Synthesis of fatty and mycolic acids	
II.A.3	3990	26	75	0	0.49	2	132	0.803	0.45454918150765466	0.5830087328032961	Aminoacyl tRNA synthases and their modification	
II.B.5	3990	27	75	0	0.51	2	133	0.797	0.4595126384307819	0.5830375412347555	Esterases and lipases	
II.C.3	3990	28	75	0	0.53	2	134	0.791	0.4644578041232414	0.5830427753887498	Murein sacculus and peptidoglycan	
II.A.7	3990	32	75	0	0.6	2	138	0.769	0.48404541146883984	0.594972484930449	RNA synthesis, RNA modification and DNA transcription	
IV.B.1.a	3990	32	75	0	0.6	2	138	0.769	0.48404541146883984	0.594972484930449	IS6110	
II.B.3	3990	34	75	0	0.64	2	140	0.758	0.4937166887480361	0.6002589225909903	Proteins, peptides and glycopeptides	
IV.B.3	3990	35	75	0	0.66	2	141	0.752	0.49852012215183944	0.6002589225909903	Phage-related functions	
IV.C.1.a	3990	38	75	0	0.71	2	144	0.738	0.5127966218877041	0.6112121351792837	PE subfamily	
I.D	3990	95	75	1	1.79	3	201	0.792	0.5276415597299671	0.6226170404813611	Amino acid biosynthesis	Rv0391/metZ
I.C	3990	45	75	0	0.85	2	151	0.702	0.5452802285937118	0.6370600690500792	Central intermediary metabolism	
IV.B.1.c	3990	52	75	0	0.98	2	158	0.671	0.5765167261254279	0.666950722380397	Others	
II.A.1	3990	58	75	0	1.09	2	164	0.647	0.6022336758384523	0.677907511508643	Ribosomal protein synthesis and modification	
I.F	3990	60	75	0	1.13	2	166	0.639	0.6105815578607678	0.677907511508643	Purines, pyrimidines, nucleosides and nucleotides	
I.G	3990	117	75	1	2.2	3	223	0.714	0.6114962586154901	0.677907511508643	Biosynthesis of cofactors, prosthetic groups and carriers	Rv0693/pqqE
IV.C.1.b	3990	61	75	0	1.15	2	167	0.635	0.614712743486651	0.677907511508643	PE_PGRS subfamily	
IV.H	3990	61	75	0	1.15	2	167	0.635	0.614712743486651	0.677907511508643	Miscellaneous transferases	
II.A.5	3990	69	75	0	1.3	2	175	0.606	0.6467214090357076	0.7066030209834583	DNA replication, repair, recombination and restriction/modification	
II.B	3990	87	75	0	1.64	2	193	0.549	0.7118613306796271	0.7706388717449174	Degradation of macromolecules	
IV.B.1	3990	90	75	0	1.69	2	196	0.542	0.7217910036199751	0.7742848947923369	IS elements	
IV.C.1	3990	99	75	0	1.86	2	205	0.518	0.7500185387847069	0.7973170051945533	PE family	
IV.C	3990	167	75	1	3.14	3	273	0.584	0.765620933083824	0.8066363402133145	PE and PPE families	Rv3135/PPE50
IV.B	3990	135	75	0	2.54	2	241	0.441	0.8409882590802004	0.8782001289510056	IS elements, Repeated sequences, and Phage	
II.C.5	3990	211	75	1	3.97	3	317	0.503	0.8585248923376523	0.8886485727705524	Other membrane proteins	Rv3200c/-
II	3990	662	75	7	12.44	9	768	0.623	0.9333370385324071	0.9538215760275494	Macromolecule metabolism	Rv0450c/mmpL4 Rv0806c/cpsY Rv1183/mmpL10 Rv2942/mmpL7 Rv2945c/lppX Rv3200c/- Rv3495c/lprN
VI	3990	606	75	6	11.39	8	712	0.597	0.937655108637252	0.9538215760275494	Unknowns	Rv0381c/- Rv0390/- Rv0999/- Rv3493c/- Rv3531c/- Rv3542c/-
II.A	3990	215	75	0	4.04	2	321	0.331	0.9481474377598108	0.9562512620141681	Synthesis and modification of macromolecules	
V	3990	915	75	8	17.2	10	1021	0.521	0.9927725101507601	0.9927725101507601	Conserved hypotheticals	Rv0495c/- Rv0805/- Rv1130/- Rv1428c/- Rv2569c/- Rv3421c/- Rv3484/cpsA Rv3492c/-
