# 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/-