# command: ../../../transit/src/transit.py pathway_enrichment resampling_glyc_chol.txt /pacific/home/ioerger/transit/src/pytransit/analysis/H37Rv_COG_roles.dat /pacific/home/ioerger/transit/src/pytransit/analysis/COG_roles.dat pathways_glyc_chol_COG.txt
# date: 2020-02-29 09:30:06.905401
# method=FISHER, PC=2
# genes with associations=2871 out of 3990 total
# significant genes (qval<0.05): 75
# 19 out of 25 pathways have >=1 gene; max has 521
#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
Q	3990	197	75	15	3.7	17	303	2.982	7.571273996993297e-06	0.00014385420594287265	Secondary metabolites biosynthesis, transport and catabolism	Rv1193/fadD36 Rv1432/- Rv2048c/pks12 Rv3494c/mce4F Rv3495c/lprN Rv3496c/mce4D Rv3497c/mce4C Rv3498c/mce4B Rv3499c/mce4A Rv3500c/yrbE4B Rv3501c/yrbE4A Rv3535c/- Rv3545c/cyp125 Rv3561/fadD3 Rv3825c/pks2
I	3990	189	75	13	3.55	15	295	2.703	8.277467327002055e-05	0.0007863593960651952	Lipid transport and metabolism	Rv0244c/fadE5 Rv1428c/- Rv1627c/- Rv3540c/ltp2 Rv3543c/fadE29 Rv3544c/fadE28 Rv3546/fadA5 Rv3551/- Rv3556c/fadA6 Rv3560c/fadE30 Rv3563/fadE32 Rv3564/fadE33 Rv3570c/-
R	3990	521	75	14	9.79	16	627	1.357	0.07023010427301078	0.3831839178397165	General function prediction only	Rv0450c/mmpL4 Rv0693/pqqE Rv0805/- Rv1129c/- Rv1130/- Rv1183/mmpL10 Rv2942/mmpL7 Rv3502c/fabG Rv3526/- Rv3542c/- Rv3549c/- Rv3553/- Rv3559c/- Rv3569c/bphD
P	3990	135	75	5	2.54	7	241	1.542	0.08067029849257189	0.3831839178397165	Inorganic ion transport and metabolism	Rv0362/mgtE Rv0390/- Rv1283c/oppB Rv2684/arsA Rv3200c/-
C	3990	222	75	6	4.17	8	328	1.297	0.15956386499457234	0.5228238409682431	Energy production and conversion	Rv0694/lldD1 Rv0761c/adhB Rv1131/gltA1 Rv3537/- Rv3571/hmp Rv3696c/glpK
V	3990	49	75	2	0.92	4	155	1.37	0.16510226556891885	0.5228238409682431	Defense mechanisms	Rv2936/drrA Rv2938/drrC
K	3990	201	75	5	3.78	7	307	1.211	0.21674193258432803	0.588299531300319	Transcription	Rv1129c/- Rv1963c/mce3R Rv2506/- Rv3484/cpsA Rv3575c/-
O	3990	88	75	2	1.65	4	194	1.096	0.29998249196309273	0.7124584184123453	Posttranslational modification, protein turnover, chaperones	Rv2462c/tig Rv3421c/-
E	3990	182	75	3	3.42	5	288	0.923	0.45943322833132577	0.8562888143841759	Amino acid transport and metabolism	Rv0391/metZ Rv2569c/- Rv3568c/bphC
U	3990	27	75	0	0.51	2	133	0.797	0.4595126384307819	0.8562888143841759	Intracellular trafficking, secretion, and vesicular transport	
D	3990	44	75	0	0.83	2	150	0.707	0.5407137623579726	0.8562888143841759	Cell cycle control, cell division, chromosome partitioning	
T	3990	99	75	1	1.86	3	205	0.777	0.5435169102008456	0.8562888143841759	Signal transduction mechanisms	Rv1626/-
G	3990	120	75	1	2.26	3	226	0.704	0.6222277049747147	0.8562888143841759	Carbohydrate transport and metabolism	Rv0485/-
F	3990	65	75	0	1.22	2	171	0.621	0.6309496527041296	0.8562888143841759	Nucleotide transport and metabolism	
M	3990	114	75	0	2.14	2	220	0.483	0.7920205612018485	0.9722196692261906	Cell wall/membrane/envelope biogenesis	
H	3990	141	75	0	2.65	2	247	0.43	0.8530500116081483	0.9722196692261906	Coenzyme transport and metabolism	
J	3990	160	75	0	3.01	2	266	0.399	0.8862120072954369	0.9722196692261906	Translation, ribosomal structure and biogenesis	
L	3990	218	75	0	4.1	2	324	0.328	0.9504107894001739	0.9722196692261906	Replication, recombination and repair	
S	3990	256	75	0	4.81	2	362	0.294	0.9722196692261906	0.9722196692261906	Function unknown