diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 66f1b180..b3ad2a38 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2272,3 +2272,4 @@ MAM00208c MAM00208 C16832 M00208 MNXM21289 m00208c m00208c MAM00209c MAM00209 C16237 M00209 MNXM96070 m00209c m00209c MAM00210c MAM00210 C16236 M00210 MNXM4090 m00210c m00210c MAM01622x MAM01622 b2coa C00877 CHEBI:15473 5280381 HC00572 b2coa MNXM214 m01622p m01622p +MAM01690m MAM01690 dhap C00111 CHEBI:16108 668 HC00109 dhap MNXM77 m01690m m01690m diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index b48534b3..349f2b01 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -108,13 +108,11 @@ MAR03751 R02660 R02660M r0560 r0560 HMR_3751 RCR14421 0 HMR_3751 MAR03783 R03172 R03172M r0603 r0603 MNXR108000 HMR_3783 RCR14424 0 HMR_3783 MAR04242 R02487 R02487M r0541 r0541 MNXR100293 HMR_4242 RCR14356 0 RHEA:30847 HMR_4242 MAR03769 R04095 R04095M r0655 r0655 MNXR95318 HMR_3769 RCR14423 0 HMR_3769 -MAR03838 r1453 HMR_3838 RCR14286 0 HMR_3838 MAR02366 r1446 r1446 0 r1446 MAR02367 r1447 r1447 0 r1447 MAR02370 r1449 r1449 0 r1449 MAR02372 r1450 r1450 0 r1450 MAR02373 r1451 r1451 0 r1451 -MAR00483 R00849 r0205 r0205 MNXR106713 HMR_0483 RCR21050 0 RHEA:18977 HMR_0483 MAR08743 R00408 SUCD1m SUCD1m MNXR99636 HMR_8743 RCR11674 0 RHEA:30343 HMR_8743 MAR05294 R00362 R00362C r1109 r1109 MNXR96731 HMR_5294 RCR11670 0 RHEA:10761 RHEA:10760 HMR_5294 MAR11421 CITL CITL MNXR96731 0 RHEA:10761 RHEA:10760 CITL @@ -401,3 +399,8 @@ MAR07851 DNDPt62m DNDPt62m MNXR97327 HMR_7851 RCR20193 0 HMR_7851 MAR07852 DNDPt63m DNDPt63m MNXR97676 HMR_7852 RCR20146 0 HMR_7852 MAR07853 DNDPt6m DNDPt6m MNXR97677 HMR_7853 RCR20194 0 HMR_7853 MAR07854 DNDPt7m DNDPt7m MNXR97175 HMR_7854 RCR20122 0 HMR_7854 + +MAR08611 R10507 PROD2m r1453 PROD2m MNXR103187 HMR_8611;HMR_3838 RCR11294;RCR14286 0 HMR_8611;HMR_3838;MAR03838 +MAR00449 R00848;R00849 r0205 R-HSA-188467 GLYC3PFADm;r0205 MNXR99875;MNXR106713 HMR_0449;HMR_0483 RCR12494;RCR21050 0 RHEA:31283;RHEA:18977 HMR_0449;HMR_0483 +MAR01169 R00849;R00848 G3PD2m R00848C r0205 G3PD2m;r0205;HMR_0482 MNXR99878;MNXR106713;MNXR192664 HMR_0483;HMR_0482 RCR21050;RCR14578 0 RHEA:18977 G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483 +MAR08111 DHAPtm DHAPtc MNXR97366 0 DHAPtc diff --git a/data/testResults/README.md b/data/testResults/README.md index 6ed6d67d..df7bdd85 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -21,12 +21,12 @@ own files. The pull request in each row is the one whose run last wrote those fi | Result file(s) | Produced by | Last updated by | | --- | --- | --- | -| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) | -| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) | -| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) | -| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) | -| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) | -| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) | +| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1028** (model QC checks) | +| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1028** (model QC checks) | +| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1028** (model QC checks) | +| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1028** (MACAW and balance) | +| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1028** (MEMOTE) | +| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1028** (gene essentiality) | ## 2. What each check means diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 5e18d532..e38a1da0 100644 --- a/data/testResults/gene-essential.csv +++ b/data/testResults/gene-essential.csv @@ -25,7 +25,7 @@ ENSG00000005187,ACSM3,TN,TN,TN,TN,TN ENSG00000005339,CREBBP,TN,TN,FN,TN,TN ENSG00000005381,MPO,TN,TN,TN,TN,TN ENSG00000005421,PON1,TN,TN,TN,TN,TN -ENSG00000005469,CROT,TN,TN,TN,TN,FP +ENSG00000005469,CROT,TN,FP,TN,TN,FP ENSG00000005471,ABCB4,TN,TN,TN,TN,TN ENSG00000005810,MYCBP2,TN,TN,TN,TN,TN ENSG00000005882,PDK2,TN,TN,TN,TN,FN @@ -134,10 +134,10 @@ ENSG00000047230,CTPS2,TN,TN,TN,TN,TN ENSG00000047249,ATP6V1H,FN,TN,FN,FN,FN ENSG00000047315,POLR2B,TP,TP,TP,TP,TP ENSG00000047410,TPR,TP,TP,TP,TP,FP -ENSG00000047457,CP,TN,TN,TN,TN,TN +ENSG00000047457,CP,FP,TN,TN,TN,TN ENSG00000048028,USP28,TN,TN,TN,TN,TN ENSG00000048392,RRM2B,FP,FP,FP,FP,FP -ENSG00000049239,H6PD,FP,FP,FP,FP,TN +ENSG00000049239,H6PD,FP,FP,FP,TN,TN ENSG00000049759,NEDD4L,TN,TN,TN,TN,TN ENSG00000049860,HEXB,TN,TN,TN,TN,TN ENSG00000050438,SLC4A8,TN,TN,TN,TN,TN @@ -163,7 +163,7 @@ ENSG00000059378,PARP12,TN,TN,TN,TN,TN ENSG00000059573,ALDH18A1,FN,TN,TN,FN,TN ENSG00000059804,SLC2A3,.,.,FN,TN,. ENSG00000060642,PIGV,FN,FN,TN,FN,TN -ENSG00000060762,MPC1,TN,TN,TN,FP,TN +ENSG00000060762,MPC1,TN,TN,TN,TN,TN ENSG00000060971,ACAA1,FP,FP,FP,FP,TP ENSG00000060982,BCAT1,TN,TN,TN,TN,FN ENSG00000061918,GUCY1B1,TN,TN,TN,TN,TN @@ -191,7 +191,7 @@ ENSG00000065911,MTHFD2,TN,TN,TN,FN,TN ENSG00000065923,SLC9A7,TN,TN,TN,TN,TN ENSG00000065989,PDE4A,TN,TN,TN,TN,TN ENSG00000066230,SLC9A3,TN,TN,TN,TN,TN -ENSG00000066322,ELOVL1,FP,FP,FP,FP,FP +ENSG00000066322,ELOVL1,FP,TN,FP,FP,FP ENSG00000066379,POLR1H,TP,TP,TP,TP,TP ENSG00000066651,TRMT11,TN,TN,TN,TN,TN ENSG00000066813,ACSM2B,TN,TN,FN,TN,TN @@ -241,14 +241,14 @@ ENSG00000071794,HLTF,TN,TN,TN,TN,TN ENSG00000071967,CYBRD1,TN,FN,TN,TN,TN ENSG00000072041,SLC6A15,TN,TN,TN,TN,TN ENSG00000072042,RDH11,TN,TN,TN,TN,TN -ENSG00000072210,ALDH3A2,TN,TN,TN,TN,TN +ENSG00000072210,ALDH3A2,TN,FP,TN,TN,FP ENSG00000072274,TFRC,FN,TN,FN,TN,TN ENSG00000072401,UBE2D1,TN,TN,TN,TN,TN ENSG00000072506,HSD17B10,TP,TP,TP,TP,FP ENSG00000072609,CHFR,TN,TN,TN,TN,TN ENSG00000072657,TRHDE,TN,TN,TN,TN,TN ENSG00000072682,P4HA2,TN,FN,TN,TN,TN -ENSG00000072778,ACADVL,FP,TN,FP,TN,TN +ENSG00000072778,ACADVL,TN,TN,TN,FP,FP ENSG00000073060,SCARB1,FP,FP,FP,FP,FP ENSG00000073417,PDE8A,TN,TN,TN,TN,TN ENSG00000073578,SDHA,TP,FP,TP,FP,TP @@ -311,7 +311,7 @@ ENSG00000081800,SLC13A1,TN,TN,TN,TN,TN ENSG00000081923,ATP8B1,TN,TN,TN,TN,TN ENSG00000082212,ME2,TN,TN,TN,TN,TN ENSG00000082996,RNF13,.,.,TN,TN,. -ENSG00000083123,BCKDHB,TN,TN,FP,FP,TN +ENSG00000083123,BCKDHB,TN,FP,TN,TN,FP ENSG00000083168,KAT6A,TN,TN,TN,TN,TN ENSG00000083223,TUT7,TN,TN,TN,TN,TN ENSG00000083444,PLOD1,TN,TN,TN,TN,FN @@ -428,7 +428,7 @@ ENSG00000100023,PPIL2,FN,FN,FN,FN,FN ENSG00000100024,UPB1,TN,TN,TN,TN,TN ENSG00000100031,GGT1,.,.,.,.,. ENSG00000100033,PRODH,TN,TN,TN,TN,TN -ENSG00000100075,SLC25A1,TN,TN,TN,TN,TN +ENSG00000100075,SLC25A1,TN,TN,TN,FP,TN ENSG00000100077,GRK3,TN,TN,TN,TN,TN ENSG00000100078,PLA2G3,TN,TN,TN,TN,TN ENSG00000100092,SH3BP1,TN,TN,TN,TN,TN @@ -448,7 +448,7 @@ ENSG00000100299,ARSA,TN,TN,TN,TN,TN ENSG00000100344,PNPLA3,TN,TN,TN,TN,TN ENSG00000100348,TXN2,FN,TN,FN,FN,FN ENSG00000100354,TNRC6B,TN,TN,TN,TN,TN -ENSG00000100372,SLC25A17,TN,TN,TN,TN,FP +ENSG00000100372,SLC25A17,TN,FP,FP,TN,FP ENSG00000100393,EP300,FN,TN,TN,TN,TN ENSG00000100412,ACO2,FN,FN,FN,FN,TN ENSG00000100413,POLR3H,TP,TP,TP,TP,TP @@ -514,7 +514,7 @@ ENSG00000102032,RENBP,TN,TN,TN,TN,TN ENSG00000102043,MTMR8,TN,TN,TN,TN,TN ENSG00000102078,SLC25A14,TN,TN,TN,TN,TN ENSG00000102100,SLC35A2,TN,TN,TN,TN,TN -ENSG00000102144,PGK1,TP,FN,TP,TP,FN +ENSG00000102144,PGK1,TP,FN,TP,FN,FN ENSG00000102172,SMS,TN,TN,TN,TN,TN ENSG00000102226,USP11,TN,TN,TN,TN,TN ENSG00000102230,PCYT1B,TN,TN,TN,TN,TN @@ -525,7 +525,7 @@ ENSG00000102393,GLA,TN,TN,TN,TN,TN ENSG00000102452,NALCN,TN,TN,TN,TN,TN ENSG00000102575,ACP5,TN,TN,TN,TN,TN ENSG00000102699,PARP4,TN,TN,TN,TN,TN -ENSG00000102743,SLC25A15,FN,TN,FN,TP,TN +ENSG00000102743,SLC25A15,FN,TN,FN,FN,FP ENSG00000102780,DGKH,TN,TN,TN,TN,TN ENSG00000102794,ACOD1,FN,TN,FN,FN,TN ENSG00000102858,MGRN1,TN,TN,TN,TN,TN @@ -567,7 +567,7 @@ ENSG00000104044,OCA2,TN,TN,TN,TN,TN ENSG00000104055,TGM5,TN,TN,TN,TN,TN ENSG00000104219,ZDHHC2,TN,TN,TN,TN,FN ENSG00000104267,CA2,TN,TN,TN,TN,TN -ENSG00000104325,DECR1,FP,TN,FP,FP,TN +ENSG00000104325,DECR1,FP,FP,FP,FP,FP ENSG00000104331,BPNT2,TN,TN,TN,TN,TN ENSG00000104343,UBE2W,.,.,TN,TN,. ENSG00000104517,UBR5,TN,TN,TN,TN,TN @@ -581,26 +581,26 @@ ENSG00000104763,ASAH1,TN,TN,TN,TN,TN ENSG00000104774,MAN2B1,TN,TN,TN,TN,TN ENSG00000104808,DHDH,TN,TN,TN,TN,TN ENSG00000104812,GYS1,TN,TN,TN,TN,TN -ENSG00000104823,ECH1,FP,TN,FP,FP,TN +ENSG00000104823,ECH1,FP,FP,FP,FP,TN ENSG00000104879,CKM,TN,TN,FN,TN,TN ENSG00000104885,DOT1L,FN,FN,TN,TN,FN ENSG00000104888,SLC17A7,TN,FN,FP,TN,TN ENSG00000104907,TRMT1,FN,FN,TN,TN,TN ENSG00000104951,IL4I1,TN,TN,TN,TN,TN ENSG00000105143,SLC1A6,TN,TN,TN,TN,TN -ENSG00000105220,GPI,TP,TN,TP,TP,TN +ENSG00000105220,GPI,TP,TN,TP,FN,TN ENSG00000105254,TBCB,FN,TN,TN,TN,FN ENSG00000105258,POLR2I,TP,TP,TP,TP,TP ENSG00000105281,SLC1A5,TN,TN,TN,TN,TN ENSG00000105355,PLIN3,TN,TN,TN,TN,TN -ENSG00000105379,ETFB,TN,TN,TN,TN,TN +ENSG00000105379,ETFB,FP,FP,FP,FP,FP ENSG00000105398,SULT2A1,TN,TN,TN,TN,TN ENSG00000105409,ATP1A3,TN,TN,TN,TN,TN ENSG00000105499,PLA2G4C,TN,TN,TN,TN,TN ENSG00000105509,HAS1,TN,TN,TN,TN,TN ENSG00000105516,DBP,TN,TN,TN,TN,TN ENSG00000105520,PLPPR2,.,.,.,.,. -ENSG00000105552,BCAT2,TN,TN,FP,FP,TN +ENSG00000105552,BCAT2,TN,FP,TN,TN,FP ENSG00000105607,GCDH,TN,TN,TN,TN,TN ENSG00000105641,SLC5A5,TN,TN,TN,TN,TN ENSG00000105647,PIK3R2,FN,TN,TN,TN,TN @@ -677,7 +677,7 @@ ENSG00000108846,ABCC3,TN,TN,TN,TN,TN ENSG00000108854,SMURF2,TN,TN,FN,TN,TN ENSG00000108932,SLC16A6,TN,TN,TN,TN,TN ENSG00000109065,NAT9,TN,TN,TN,TN,TN -ENSG00000109107,ALDOC,TN,TN,FP,FP,TN +ENSG00000109107,ALDOC,TN,TN,FP,TN,TN ENSG00000109181,UGT2B10,.,.,.,.,. ENSG00000109189,USP46,TN,TN,TN,TN,TN ENSG00000109193,SULT1E1,TN,TN,TN,TN,TN @@ -700,7 +700,7 @@ ENSG00000109956,B3GAT1,TN,TN,TN,TN,TN ENSG00000110013,SIAE,TN,TN,TN,TN,TN ENSG00000110066,KMT5B,FN,FN,TN,TN,FN ENSG00000110080,ST3GAL4,TN,TN,TN,TN,TN -ENSG00000110090,CPT1A,FP,TN,FP,FP,TN +ENSG00000110090,CPT1A,FP,FP,FP,FP,TN ENSG00000110195,FOLR1,TN,TN,TN,TN,TN ENSG00000110203,FOLR3,TN,TN,TN,TN,TN ENSG00000110245,APOC3,TN,TN,TN,TN,TN @@ -747,7 +747,7 @@ ENSG00000111684,LPCAT3,TN,TN,TN,TN,TN ENSG00000111696,NT5DC3,TN,TN,TN,TN,TN ENSG00000111700,SLCO1B3,TN,TN,TN,TN,TN ENSG00000111713,GYS2,TN,TN,TN,TN,TN -ENSG00000111716,LDHB,.,.,TN,TN,. +ENSG00000111716,LDHB,.,.,TN,TN,P ENSG00000111726,CMAS,TN,TN,TN,TN,TN ENSG00000111728,ST8SIA1,TN,TN,TN,TN,TN ENSG00000111732,AICDA,TN,TN,TN,TN,TN @@ -779,7 +779,7 @@ ENSG00000112759,SLC29A1,TN,TN,TN,TN,TN ENSG00000112874,NUDT12,TN,TN,TN,TN,TN ENSG00000112893,MAN2A1,TN,TN,TN,TN,TN ENSG00000112941,TENT4A,TN,TN,TN,TN,TN -ENSG00000112972,HMGCS1,TP,TP,TP,FN,TN +ENSG00000112972,HMGCS1,FN,TP,TP,FN,FP ENSG00000112992,NNT,TN,TN,TN,TN,TN ENSG00000113013,HSPA9,FN,FN,FN,FN,FN ENSG00000113073,SLC4A9,TN,FN,TN,TN,TN @@ -877,14 +877,14 @@ ENSG00000116459,ATP5PB,TP,TP,TP,TP,FP ENSG00000116514,RNF19B,TN,TN,TN,TN,TN ENSG00000116539,ASH1L,TN,TN,TN,TN,TN ENSG00000116649,SRM,TN,TN,TN,TN,TN -ENSG00000116704,SLC35D1,TN,TN,FP,FP,TN +ENSG00000116704,SLC35D1,TN,FP,TN,FP,TN ENSG00000116711,PLA2G4A,TN,TN,TN,TN,TN ENSG00000116745,RPE65,TN,TN,TN,TN,TN ENSG00000116748,AMPD1,TN,TN,TN,TN,TN ENSG00000116761,CTH,TN,TN,TN,TN,TN ENSG00000116771,AGMAT,TN,TN,TN,TN,TN ENSG00000116791,CRYZ,TN,TN,TN,TN,TN -ENSG00000116906,GNPAT,TN,TN,FP,TN,TN +ENSG00000116906,GNPAT,FP,TN,TN,TN,FP ENSG00000116981,NT5C1A,TN,TN,TN,TN,TN ENSG00000116984,MTR,TN,TN,TN,TN,TN ENSG00000117009,KMO,TN,TN,TN,TN,TN @@ -899,14 +899,14 @@ ENSG00000117308,GALE,TN,TN,TN,TN,TN ENSG00000117394,SLC2A1,TN,TN,TN,TN,TN ENSG00000117410,ATP6V0B,FN,FN,FN,FN,FN ENSG00000117411,B4GALT2,TN,TN,TN,TN,FN -ENSG00000117448,AKR1A1,TN,TN,FP,TN,TN +ENSG00000117448,AKR1A1,FP,TN,TN,FP,FP ENSG00000117450,PRDX1,TN,TN,FN,TN,TN ENSG00000117461,PIK3R3,TN,TN,TN,TN,TN ENSG00000117479,SLC19A2,TN,FP,FP,FP,FP ENSG00000117480,FAAH,TN,TN,TN,TN,TN ENSG00000117528,ABCD3,TN,TN,TN,TN,TN ENSG00000117543,DPH5,FN,TN,FN,FN,TN -ENSG00000117592,PRDX6,TN,FP,FP,FP,TN +ENSG00000117592,PRDX6,TN,TN,FP,FP,FP ENSG00000117594,HSD11B1,TN,TN,TN,TN,TN ENSG00000117600,PLPPR4,.,.,.,.,. ENSG00000117643,MAN1C1,TN,TN,TN,TN,TN @@ -954,7 +954,7 @@ ENSG00000120137,PANK3,TN,TN,TN,TN,TN ENSG00000120253,NUP43,TP,FP,TP,TP,TP ENSG00000120254,MTHFD1L,TN,TN,TN,TN,FN ENSG00000120265,PCMT1,TN,TN,TN,TN,TN -ENSG00000120329,SLC25A2,TN,TN,FP,FP,TN +ENSG00000120329,SLC25A2,TN,FP,TN,TN,FP ENSG00000120437,ACAT2,FP,FP,FP,FP,FP ENSG00000120563,LYZL1,.,.,.,.,. ENSG00000120697,ALG5,TN,TN,TN,TN,TN @@ -986,7 +986,7 @@ ENSG00000122642,FKBP9,TN,TN,TN,TN,TN ENSG00000122643,NT5C3A,.,.,TN,TN,. ENSG00000122678,POLM,TN,TN,TN,TN,TN ENSG00000122729,ACO1,TN,TN,TN,TN,TN -ENSG00000122787,AKR1D1,TN,TN,TN,TN,TN +ENSG00000122787,AKR1D1,TN,TN,TN,FP,TN ENSG00000122824,NUDT10,.,.,.,.,. ENSG00000122863,CHST3,TN,TN,TN,TN,TN ENSG00000122884,P4HA1,TN,TN,TN,TN,TN @@ -1000,7 +1000,7 @@ ENSG00000123453,SARDH,TN,TN,TN,TN,TN ENSG00000123454,DBH,TN,TN,TN,TN,TN ENSG00000123505,AMD1,TN,FP,FN,TN,FP ENSG00000123552,USP45,TN,TN,TN,TN,TN -ENSG00000123643,SLC36A1,TN,FP,FP,FP,TN +ENSG00000123643,SLC36A1,TN,FP,FP,FP,FP ENSG00000123684,LPGAT1,TN,TN,TN,TN,TN ENSG00000123739,PLA2G12A,.,.,TN,TN,. ENSG00000123836,PFKFB2,TN,TN,TN,TN,TN @@ -1035,8 +1035,8 @@ ENSG00000124615,MOCS1,TN,TN,TN,TN,TN ENSG00000124713,GNMT,TN,TN,TN,TN,TN ENSG00000124767,GLO1,TN,TN,TN,TN,TN ENSG00000124789,NUP153,TP,TP,TP,TP,TP -ENSG00000125166,GOT2,TN,TN,FP,FP,TN -ENSG00000125246,CLYBL,TN,TN,FP,FP,TN +ENSG00000125166,GOT2,TN,FP,TN,TN,FP +ENSG00000125246,CLYBL,TN,TN,FP,TN,TN ENSG00000125255,SLC10A2,TN,TN,TN,TN,TN ENSG00000125257,ABCC4,TN,TN,TN,TN,TN ENSG00000125356,NDUFA1,TN,TN,FN,TN,TN @@ -1087,7 +1087,7 @@ ENSG00000128708,HAT1,TN,TN,TN,TN,TN ENSG00000128731,HERC2,TN,TN,TN,TN,TN ENSG00000128918,ALDH1A2,FP,FP,TN,TN,TN ENSG00000128928,IVD,TN,TN,TN,TN,TN -ENSG00000128951,DUT,TN,TN,TN,TN,TN +ENSG00000128951,DUT,TN,TN,FP,FP,FP ENSG00000129128,SPCS3,TP,TP,TP,TP,TP ENSG00000129151,BBOX1,FP,FP,FP,FP,FP ENSG00000129167,TPH1,TN,TN,TN,TN,TN @@ -1116,7 +1116,7 @@ ENSG00000130227,XPO7,TN,TN,TN,TN,TN ENSG00000130234,ACE2,TN,TN,TN,TN,TN ENSG00000130304,SLC27A1,TN,TN,TN,TN,TN ENSG00000130309,COLGALT1,TN,TN,TN,TN,TN -ENSG00000130313,PGLS,TN,FN,FN,TP,TN +ENSG00000130313,PGLS,TN,FN,FN,FN,TN ENSG00000130377,ACSBG2,TN,TN,TN,TN,TN ENSG00000130383,FUT5,TN,TN,TN,TN,TN ENSG00000130414,NDUFA10,TN,FN,FN,TN,TN @@ -1172,7 +1172,7 @@ ENSG00000131873,CHSY1,TN,TN,TN,TN,TN ENSG00000131979,GCH1,FP,FP,FP,FP,FP ENSG00000132164,SLC6A11,TN,TN,TN,TN,TN ENSG00000132182,NUP210,FP,FP,FP,FP,FP -ENSG00000132196,HSD17B7,P,P,P,P,P +ENSG00000132196,HSD17B7,.,P,P,P,P ENSG00000132256,TRIM5,TN,TN,TN,TN,TN ENSG00000132330,SCLY,TN,TN,TN,TN,TN ENSG00000132376,INPP5K,TN,TN,TN,TN,TN @@ -1254,7 +1254,7 @@ ENSG00000135241,PNPLA8,TN,FN,TN,TN,TN ENSG00000135318,NT5E,TN,TN,TN,TN,TN ENSG00000135390,ATP5MC2,FP,FP,TP,TP,FP ENSG00000135423,GLS2,FN,TN,TN,TN,TN -ENSG00000135437,RDH5,TN,TP,FP,TP,FP +ENSG00000135437,RDH5,FP,TP,FP,TP,FP ENSG00000135454,B4GALNT1,TN,TN,TN,TN,TN ENSG00000135587,SMPD2,TN,TN,TN,TN,TN ENSG00000135655,USP15,TN,TN,TN,TN,TN @@ -1299,7 +1299,7 @@ ENSG00000136840,ST6GALNAC4,TN,TN,TN,TN,TN ENSG00000136856,SLC2A8,TN,TN,TN,TN,TN ENSG00000136868,SLC31A1,TN,TN,FN,TN,TN ENSG00000136872,ALDOB,TN,TN,TN,TN,TN -ENSG00000136877,FPGS,FN,FP,FP,TP,TN +ENSG00000136877,FPGS,FN,FP,FP,TP,FP ENSG00000136878,USP20,TN,TN,TN,TN,TN ENSG00000136881,BAAT,TN,TN,TN,TN,TN ENSG00000136888,ATP6V1G1,FN,TN,FN,TN,FN @@ -1307,7 +1307,7 @@ ENSG00000136908,DPM2,TN,FN,TN,TN,TN ENSG00000136943,CTSV,TN,TN,TN,TN,TN ENSG00000136960,ENPP2,TN,TN,TN,TN,TN ENSG00000137054,POLR1E,TP,TP,TP,FP,TP -ENSG00000137106,GRHPR,TN,TN,TN,TN,TN +ENSG00000137106,GRHPR,TN,TN,TN,TN,FP ENSG00000137124,ALDH1B1,TN,TN,TN,TN,TN ENSG00000137168,PPIL1,TN,TN,TN,TN,TN ENSG00000137198,GMPR,TN,TN,TN,TN,TN @@ -1317,7 +1317,7 @@ ENSG00000137364,TPMT,TN,TN,TN,TN,TN ENSG00000137392,CLPS,TN,TN,TN,TN,TN ENSG00000137393,RNF144B,TN,TN,TN,TN,TN ENSG00000137491,SLCO2B1,TN,TN,TN,TN,TN -ENSG00000137563,GGH,TN,TP,FP,FP,TN +ENSG00000137563,GGH,TN,TP,FP,FP,FP ENSG00000137714,FDX1,TN,TN,.,TN,TN ENSG00000137731,FXYD2,TN,TN,TN,TN,TN ENSG00000137767,SQOR,.,.,.,.,. @@ -1325,13 +1325,13 @@ ENSG00000137770,CTDSPL2,.,.,TN,TN,. ENSG00000137817,PARP6,TN,TN,TN,TN,TN ENSG00000137825,ITPKA,TN,TN,TN,TN,TN ENSG00000137841,PLCB2,TN,TN,TN,FN,TN -ENSG00000137857,DUOX1,TN,TN,TN,FP,TN +ENSG00000137857,DUOX1,TN,TN,TN,TN,TN ENSG00000137860,SLC28A2,TN,TN,TN,TN,TN ENSG00000137868,STRA6,TN,TN,TN,TN,TN ENSG00000137869,CYP19A1,TN,TN,TN,TN,TN ENSG00000137944,KYAT3,TN,TN,TN,TN,TN ENSG00000137968,SLC44A5,TN,TN,TN,TN,TN -ENSG00000137992,DBT,TN,TN,FP,FP,TN +ENSG00000137992,DBT,TN,FP,TN,TN,FP ENSG00000137996,RTCA,TN,TN,TN,TN,TN ENSG00000138018,SELENOI,TN,TN,TN,TN,TN ENSG00000138029,HADHB,FP,FP,FP,FP,FP @@ -1354,7 +1354,7 @@ ENSG00000138376,BARD1,TN,FN,FN,FN,FN ENSG00000138398,PPIG,TN,TN,TN,TN,TN ENSG00000138400,MDH1B,TN,TN,TN,TN,TN ENSG00000138411,HECW2,TN,TN,TN,TN,TN -ENSG00000138413,IDH1,TN,TN,TN,TN,TN +ENSG00000138413,IDH1,TN,TN,TN,FP,TN ENSG00000138449,SLC40A1,TN,TN,TN,TN,TN ENSG00000138496,PARP9,TN,TN,TN,TN,TN ENSG00000138592,USP8,FN,FN,TN,FN,FN @@ -1414,7 +1414,7 @@ ENSG00000140284,SLC27A2,TN,TN,TN,TN,TN ENSG00000140287,HDC,TN,TN,TN,TN,TN ENSG00000140297,GCNT3,TN,TN,TN,TN,TN ENSG00000140367,UBE2Q2,TN,TN,TN,TN,TN -ENSG00000140374,ETFA,TN,TN,TN,TN,TN +ENSG00000140374,ETFA,FP,FP,FP,FP,FP ENSG00000140400,MAN2C1,TN,TN,TN,TN,TN ENSG00000140455,USP3,TN,TN,TN,TN,TN ENSG00000140459,CYP11A1,FN,TN,TN,TN,TN @@ -1475,7 +1475,7 @@ ENSG00000143036,SLC44A3,TN,TN,TN,TN,TN ENSG00000143149,ALDH9A1,FP,FP,FP,FP,FP ENSG00000143153,ATP1B1,TN,TN,TN,TN,TN ENSG00000143156,NME7,TN,TN,TN,TN,TN -ENSG00000143158,MPC2,TN,TN,TN,FP,TN +ENSG00000143158,MPC2,TN,TN,TN,TN,TN ENSG00000143179,UCK2,TN,TN,TN,TN,TN ENSG00000143198,MGST3,TN,TN,TN,TN,TN ENSG00000143199,ADCY10,TN,TN,TN,TN,TN @@ -1502,7 +1502,7 @@ ENSG00000143641,GALNT2,TN,TN,TN,TN,TN ENSG00000143653,SCCPDH,TN,TN,TN,TN,TN ENSG00000143753,DEGS1,TN,FP,TN,FP,FP ENSG00000143772,ITPKB,TN,TN,TN,TN,TN -ENSG00000143774,GUK1,TP,FN,TP,TP,FN +ENSG00000143774,GUK1,TP,FN,FN,TP,TP ENSG00000143797,MBOAT2,TN,FN,TN,TN,TN ENSG00000143799,PARP1,TN,TN,TN,TN,TN ENSG00000143811,PYCR2,TN,TN,TN,TN,TN @@ -1613,7 +1613,7 @@ ENSG00000148834,GSTO1,TN,TN,FN,TN,TN ENSG00000149016,TUT1,FN,FN,FN,FN,FN ENSG00000149084,HSD17B12,FP,TP,FP,TP,FP ENSG00000149089,APIP,.,P,TN,TN,P -ENSG00000149091,DGKZ,FP,TN,TN,TN,TN +ENSG00000149091,DGKZ,TN,TN,TN,TN,TN ENSG00000149124,GLYAT,TN,TN,TN,TN,TN ENSG00000149150,SLC43A1,TN,TN,TN,TN,TN ENSG00000149313,AASDHPPT,FN,FN,FN,FN,FN @@ -1640,7 +1640,7 @@ ENSG00000151012,SLC7A11,TN,TN,TN,TN,TN ENSG00000151092,NGLY1,TN,FN,FN,TN,TN ENSG00000151093,OXSM,FN,FN,TN,TN,FN ENSG00000151148,UBE3B,TN,TN,TN,TN,TN -ENSG00000151151,IPMK,FP,TN,TN,TN,TN +ENSG00000151151,IPMK,TN,TN,TN,TN,TN ENSG00000151224,MAT1A,TN,TN,TN,TN,TN ENSG00000151229,SLC2A13,TN,FN,TN,TN,TN ENSG00000151348,EXT2,TN,TN,TN,TN,TN @@ -1726,7 +1726,7 @@ ENSG00000155897,ADCY8,TN,TN,TN,TN,TN ENSG00000156006,NAT2,TN,TN,TN,TN,TN ENSG00000156096,UGT2B4,TN,TN,TN,TN,TN ENSG00000156110,ADK,TN,TN,TN,TN,TN -ENSG00000156136,DCK,FP,FP,TN,TN,FP +ENSG00000156136,DCK,TN,TN,FP,FP,FP ENSG00000156219,ART3,TN,TN,TN,TN,TN ENSG00000156222,SLC28A1,TN,TN,TN,TN,TN ENSG00000156256,USP16,TN,TN,TN,TN,TN @@ -1753,7 +1753,7 @@ ENSG00000157045,NTAN1,TN,TN,TN,TN,TN ENSG00000157064,NMNAT2,TN,TN,TN,TN,TN ENSG00000157087,ATP2B2,TN,TN,TN,TN,TN ENSG00000157103,SLC6A1,TN,TN,TN,TN,TN -ENSG00000157184,CPT2,FP,TN,FP,FP,TN +ENSG00000157184,CPT2,FP,FP,FP,FP,TN ENSG00000157326,DHRS4,TN,TN,TN,TN,TN ENSG00000157349,DDX19B,TP,FP,FP,FP,FP ENSG00000157350,ST3GAL2,TN,TN,TN,TN,TN @@ -1798,7 +1798,7 @@ ENSG00000159339,PADI4,TN,TN,TN,TN,TN ENSG00000159348,CYB5R1,TN,TN,TN,TN,TN ENSG00000159398,CES5A,TN,TN,TN,TN,TN ENSG00000159399,HK2,FN,TN,TN,TN,TN -ENSG00000159423,ALDH4A1,FP,TN,FP,FP,TN +ENSG00000159423,ALDH4A1,FP,FP,FP,TN,FP ENSG00000159433,STARD9,TN,TN,TN,TN,TN ENSG00000159445,THEM4,TN,TN,TN,TN,TN ENSG00000159459,UBR1,TN,TN,TN,TN,TN @@ -1820,7 +1820,7 @@ ENSG00000160191,PDE9A,TN,TN,TN,TN,TN ENSG00000160194,NDUFV3,TN,TN,TN,TN,TN ENSG00000160200,CBS,TN,TN,TN,TN,TN ENSG00000160209,PDXK,FP,FP,FP,FP,FP -ENSG00000160211,G6PD,FN,FN,FN,TP,FN +ENSG00000160211,G6PD,FN,FN,FN,FN,FN ENSG00000160216,AGPAT3,TN,TN,TN,TN,TN ENSG00000160282,FTCD,TN,TN,TN,TN,FN ENSG00000160285,LSS,FP,TP,FP,FP,FP @@ -1844,7 +1844,7 @@ ENSG00000161267,BDH1,TN,TN,TN,TN,TN ENSG00000161281,COX7A1,TN,TN,TN,TN,TN ENSG00000161513,FDXR,TN,TN,FN,FN,TN ENSG00000161533,ACOX1,FP,TP,FP,FP,FP -ENSG00000161653,NAGS,TN,TN,FP,FP,TN +ENSG00000161653,NAGS,TN,FP,TN,TN,FP ENSG00000161714,PLCD3,TN,TN,TN,TN,TN ENSG00000161798,AQP5,TN,FN,TN,TN,TN ENSG00000161896,IP6K3,FN,TN,TN,TN,TN @@ -1854,11 +1854,11 @@ ENSG00000162040,HS3ST6,TN,TN,TN,TN,TN ENSG00000162066,AMDHD2,TN,TN,TN,TN,FN ENSG00000162104,ADCY9,TN,TN,TN,TN,TN ENSG00000162139,NEU3,TN,TN,TN,TN,TN -ENSG00000162174,ASRGL1,TN,TN,FP,TP,TN +ENSG00000162174,ASRGL1,TN,FP,TN,FN,FP ENSG00000162298,SYVN1,FN,FN,TN,FN,TN ENSG00000162341,TPCN2,TN,TN,TN,TN,TN ENSG00000162365,CYP4A22,TN,TN,TN,TN,TN -ENSG00000162368,CMPK1,P,P,FN,TP,P +ENSG00000162368,CMPK1,P,.,TP,TP,P ENSG00000162383,SLC1A7,FN,TN,TN,TN,TN ENSG00000162390,ACOT11,TN,TN,TN,TN,TN ENSG00000162402,USP24,TN,TN,TN,TN,TN @@ -2003,14 +2003,14 @@ ENSG00000165970,SLC6A5,TN,FN,TN,TN,TN ENSG00000165996,HACD1,TN,TN,TN,TN,TN ENSG00000166016,ABTB2,TN,TN,TN,TN,TN ENSG00000166035,LIPC,TN,TN,TN,TN,TN -ENSG00000166123,GPT2,TN,TN,FP,FP,TN +ENSG00000166123,GPT2,TN,FP,TN,TN,FP ENSG00000166126,AMN,TN,TN,TN,TN,TN ENSG00000166135,HIF1AN,TN,TN,TN,TN,TN ENSG00000166136,NDUFB8,FN,FN,FN,TN,FN ENSG00000166165,CKB,TN,TN,TN,TN,TN ENSG00000166169,POLL,TN,TN,TN,TN,TN ENSG00000166183,ASPG,TN,TN,TN,TN,TN -ENSG00000166224,SGPL1,FP,TP,TN,FP,TN +ENSG00000166224,SGPL1,TN,TP,FP,FP,TN ENSG00000166228,PCBD1,TN,TN,TN,TN,TN ENSG00000166262,FAM227B,TN,TN,TN,TN,TN ENSG00000166311,SMPD1,TN,TN,TN,TN,TN @@ -2124,7 +2124,7 @@ ENSG00000169105,CHST14,TN,TN,TN,TN,TN ENSG00000169154,GOT1L1,TN,TN,TN,TN,TN ENSG00000169169,CPT1C,TN,TN,TN,TN,TN ENSG00000169180,XPO6,TN,TN,TN,TN,FN -ENSG00000169239,CA5B,FP,FP,FP,FP,TN +ENSG00000169239,CA5B,FP,FP,FP,TN,TN ENSG00000169255,B3GALNT1,TN,TN,TN,TN,TN ENSG00000169299,PGM2,TN,TN,TN,TN,TN ENSG00000169359,SLC33A1,TN,TN,TN,TN,TN @@ -2189,7 +2189,7 @@ ENSG00000171408,PDE7B,TN,TN,TN,TN,TN ENSG00000171428,NAT1,.,.,.,.,. ENSG00000171453,POLR1C,TP,TP,TP,TP,TP ENSG00000171497,PPID,TN,TN,TN,TN,TN -ENSG00000171503,ETFDH,TN,TN,TN,TN,TN +ENSG00000171503,ETFDH,FP,FP,FP,FP,FP ENSG00000171560,FGA,TN,TN,TN,TN,TN ENSG00000171608,PIK3CD,TN,TN,TN,TN,TN ENSG00000171612,SLC25A33,TN,TN,TN,TN,TN @@ -2257,7 +2257,7 @@ ENSG00000173486,FKBP2,TN,TN,TN,TN,TN ENSG00000173540,GMPPB,FN,FN,FN,FN,FN ENSG00000173597,SULT1B1,TN,TN,TN,TN,TN ENSG00000173598,NUDT4,TN,FN,FN,TN,TN -ENSG00000173599,PC,FP,FP,TN,TP,TN +ENSG00000173599,PC,FP,FP,FP,FN,TN ENSG00000173610,UGT2A1,TN,TN,TN,TN,TN ENSG00000173614,NMNAT1,TN,TN,TN,TN,TN ENSG00000173627,APOBEC4,TN,TN,TN,FN,TN @@ -2333,7 +2333,7 @@ ENSG00000177054,ZDHHC13,TN,TN,TN,TN,TN ENSG00000177076,ACER2,TN,TN,TN,TN,TN ENSG00000177084,POLE,FN,TN,FN,TN,FN ENSG00000177108,ZDHHC22,TN,TN,TN,TN,TN -ENSG00000177156,TALDO1,TN,TN,FP,FP,TN +ENSG00000177156,TALDO1,TN,TN,FP,TN,TN ENSG00000177191,B3GNT8,TN,TN,TN,TN,TN ENSG00000177192,PUS1,FN,TN,TN,TN,TN ENSG00000177239,MAN1B1,TN,TN,TN,TN,TN @@ -2341,7 +2341,7 @@ ENSG00000177414,UBE2U,.,.,TN,TN,. ENSG00000177465,ACOT4,TN,TN,TN,TN,TN ENSG00000177542,SLC25A22,FN,TN,TN,TN,FN ENSG00000177628,GBA,TN,TN,TN,TN,TN -ENSG00000177646,ACAD9,TP,TN,TP,TN,TN +ENSG00000177646,ACAD9,TP,FP,TP,TN,TN ENSG00000177666,PNPLA2,FN,TN,TN,TN,TN ENSG00000177669,MBOAT4,TN,TN,TN,TN,FN ENSG00000177700,POLR2L,TP,TP,TP,TP,TP @@ -2350,7 +2350,7 @@ ENSG00000178035,IMPDH2,FN,TN,FN,TN,TN ENSG00000178127,NDUFV2,TN,TN,FN,TN,TN ENSG00000178234,GALNT11,TN,TN,TN,TN,TN ENSG00000178445,GLDC,TN,TN,TN,FP,TN -ENSG00000178537,SLC25A20,FP,FP,FP,TN,FP +ENSG00000178537,SLC25A20,FP,FP,FP,FP,FP ENSG00000178685,PARP10,TN,TN,TN,TN,TN ENSG00000178700,DHFR2,.,.,.,.,. ENSG00000178741,COX5A,FP,FP,TP,FP,TP @@ -2408,11 +2408,11 @@ ENSG00000181873,IBA57,FN,FN,FN,FN,TN ENSG00000181915,ADO,TN,TN,TN,TN,FN ENSG00000182022,CHST15,TN,TN,TN,TN,TN ENSG00000182050,MGAT4C,TN,TN,TN,TN,TN -ENSG00000182054,IDH2,TN,TN,FN,FN,TN +ENSG00000182054,IDH2,TN,TN,FN,TP,TN ENSG00000182156,ENPP7,TN,FN,TN,TN,TN ENSG00000182179,UBA7,TN,TN,TN,TN,TN ENSG00000182197,EXT1,TN,TN,TN,TN,TN -ENSG00000182199,SHMT2,TN,TN,FP,FP,TN +ENSG00000182199,SHMT2,TN,FP,TN,TN,FP ENSG00000182224,CYB5D1,TN,TN,TN,TN,TN ENSG00000182247,UBE2E2,TN,TN,TN,TN,TN ENSG00000182272,B4GALNT4,FN,TN,TN,TN,TN @@ -2588,7 +2588,7 @@ ENSG00000197253,TPSB2,.,.,.,.,. ENSG00000197296,FITM2,FN,FN,TN,TN,TN ENSG00000197323,TRIM33,TN,TN,TN,TN,TN ENSG00000197355,UAP1L1,TN,TN,TN,TN,TN -ENSG00000197375,SLC22A5,TP,TP,TP,FP,FP +ENSG00000197375,SLC22A5,TP,FN,TP,FP,FP ENSG00000197406,DIO3,TN,TN,TN,TN,TN ENSG00000197408,CYP2B6,TN,TN,TN,TN,TN ENSG00000197416,FABP12,TN,TN,FN,TN,TN @@ -2624,7 +2624,7 @@ ENSG00000198077,CYP2A7,TN,TN,TN,TN,FN ENSG00000198088,NUP62CL,TN,TN,TN,TN,TN ENSG00000198099,ADH4,TN,TN,TN,TN,TN ENSG00000198108,CHSY3,TN,TN,TN,TN,TN -ENSG00000198130,HIBCH,TN,TN,TN,FP,TN +ENSG00000198130,HIBCH,TN,TN,TN,TN,TN ENSG00000198162,MAN1A2,TN,TN,TN,TN,TN ENSG00000198189,HSD17B11,TN,TN,TN,TN,TN ENSG00000198203,SULT1C2,TN,TN,TN,TN,TN @@ -2735,7 +2735,7 @@ ENSG00000223443,USP17L2,.,.,.,.,. ENSG00000223572,CKMT1A,.,.,.,.,. ENSG00000223802,CERS1,TN,TN,TN,TN,TN ENSG00000224586,GPX5,TN,TN,TN,TN,TN -ENSG00000225697,SLC26A6,TN,TN,TN,TN,TN +ENSG00000225697,SLC26A6,TN,TN,TN,TN,FP ENSG00000226784,PGAM4,.,.,.,.,. ENSG00000227140,USP17L5,.,.,.,.,. ENSG00000227471,AKR1B15,.,.,.,.,. @@ -2779,7 +2779,7 @@ ENSG00000241635,UGT1A1,.,.,.,.,. ENSG00000241644,INMT,TN,TN,TN,TN,TN ENSG00000241837,ATP5PO,P,P,TP,TP,P ENSG00000241878,PISD,TN,TN,FN,FN,FN -ENSG00000241935,HOGA1,FP,TN,TN,FP,TN +ENSG00000241935,HOGA1,FP,FP,FP,TN,FP ENSG00000241973,PI4KA,TN,FN,FN,FN,FN ENSG00000242110,AMACR,TN,TN,TN,TN,TN ENSG00000242366,UGT1A8,.,.,.,.,. @@ -2790,7 +2790,7 @@ ENSG00000243480,AMY2A,.,.,.,.,. ENSG00000243678,NME2,TN,TN,TN,TN,TN ENSG00000243708,PLA2G4B,TN,TN,TN,TN,TN ENSG00000243955,GSTA1,.,.,.,.,. -ENSG00000243989,ACY1,TN,TN,FP,FP,TN +ENSG00000243989,ACY1,TN,FP,TN,TN,TN ENSG00000244005,NFS1,FN,FN,FN,FN,FN ENSG00000244038,DDOST,FN,FN,FN,FN,FN ENSG00000244067,GSTA2,.,.,.,.,. @@ -2799,7 +2799,7 @@ ENSG00000244474,UGT1A4,.,.,.,.,. ENSG00000244486,SCARF2,TN,TN,TN,TN,TN ENSG00000247626,MARS2,FN,FN,FN,FN,TN ENSG00000247746,USP51,TN,TN,TN,TN,TN -ENSG00000248098,BCKDHA,TN,TN,FP,FP,TN +ENSG00000248098,BCKDHA,TN,FP,TN,TN,FP ENSG00000248144,ADH1C,TN,TN,TN,TN,TN ENSG00000248933,USP17L22,.,.,.,.,. ENSG00000249222,ATP5MGL,P,P,TP,FP,P @@ -2844,6 +2844,6 @@ ENSG00000277161,PIGW,TN,TN,TN,TN,TN ENSG00000277494,GPIHBP1,TN,TN,TN,TN,TN ENSG00000277893,SRD5A2,.,.,.,.,. ENSG00000278540,ACACA,TP,TP,FP,FP,TP -ENSG00000281500,SLC37A4,P,P,P,P,. +ENSG00000281500,SLC37A4,P,P,P,P,P ENSG00000288702,UGT1A3,.,.,.,.,. ENSG00000288705,UGT1A5,.,.,.,.,. diff --git a/data/testResults/gene-essential_summary.md b/data/testResults/gene-essential_summary.md index 5a4f74d3..a989b0da 100644 --- a/data/testResults/gene-essential_summary.md +++ b/data/testResults/gene-essential_summary.md @@ -2,9 +2,9 @@ | cellLine | TP | TN | FP | FN | accuracy | sensitivity | specificity | F1 | MCC | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | -| DLD1 | 125 | 2172 | 124 | 224 | 0.8684 | 0.3582 | 0.946 | 0.4181 | 0.3525 | -| GBM | 111 | 2145 | 138 | 251 | 0.8529 | 0.3066 | 0.9396 | 0.3633 | 0.2897 | -| HCT116 | 141 | 2189 | 130 | 246 | 0.861 | 0.3643 | 0.9439 | 0.4286 | 0.3595 | -| HELA | 114 | 2233 | 164 | 197 | 0.8667 | 0.3666 | 0.9316 | 0.3871 | 0.3132 | -| RPE1 | 86 | 2183 | 162 | 214 | 0.8578 | 0.2867 | 0.9309 | 0.3139 | 0.2367 | -| all | 59 | 2355 | 159 | 69 | 0.9137 | 0.4609 | 0.9368 | 0.341 | 0.3103 | +| DLD1 | 124 | 2170 | 126 | 225 | 0.8673 | 0.3553 | 0.9451 | 0.414 | 0.3475 | +| GBM | 110 | 2123 | 160 | 252 | 0.8442 | 0.3039 | 0.9299 | 0.3481 | 0.2654 | +| HCT116 | 141 | 2195 | 124 | 246 | 0.8633 | 0.3643 | 0.9465 | 0.4325 | 0.3662 | +| HELA | 108 | 2243 | 154 | 203 | 0.8682 | 0.3473 | 0.9358 | 0.377 | 0.3052 | +| RPE1 | 87 | 2154 | 191 | 213 | 0.8473 | 0.29 | 0.9186 | 0.301 | 0.2156 | +| all | 59 | 2351 | 163 | 69 | 0.9122 | 0.4609 | 0.9352 | 0.3371 | 0.3066 | diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index 5b8d58da..72c6151d 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -632,7 +632,7 @@ MAR08607,MAM01016c + MAM01975c + 2 MAM02039c --> MAM01974c + MAM02471c,ok,ok,ok, MAR08608,MAM01742c + MAM02630c --> MAM00558c + MAM02039c + MAM02041c,MAM00558c,ok,ok,ok,N/A MAR08609,MAM00559m + 2 MAM02039m + MAM02555m --> MAM02554m + MAM02770m,ok,ok,ok,ok,N/A MAR08610,MAM01802c + MAM02770c --> MAM00559c + MAM01803c + MAM02039c,ok,ok,ok,ok,N/A -MAR08611,MAM01802m + MAM02770m --> MAM00559m + MAM01803m + MAM02039m,ok,ok,ok,ok,N/A +MAR03838,MAM02770m + MAM03103m --> MAM00559m + MAM02039m + MAM03102m,ok,ok,ok,ok,N/A MAR04285,MAM02040m + MAM02552m + MAM02942m --> 2 MAM02039m + MAM02553m + MAM02943m,ok,ok,ok,ok,N/A MAR00457,MAM01371c + MAM01982c --> MAM00913c + MAM01285c + MAM02039c,ok,ok,ok,ok,N/A MAR00460,MAM01371m + MAM01982m --> MAM00913m + MAM01285m + MAM02039m,ok,ok,ok,ok,N/A @@ -2474,7 +2474,7 @@ MAR00001,MAM01570e --> MAM01569e + 77243 MAM02956e,ok,ok,ok,ok,N/A MAR00002,MAM02040e + MAM02956e --> MAM00234e + MAM01807e,ok,ok,ok,ok,N/A MAR00003,MAM00234e + MAM02040e --> MAM00503e + MAM01807e,ok,ok,ok,ok,N/A MAR00005,MAM00503c + MAM02040c --> MAM01807c + MAM01983c,ok,ok,ok,ok,N/A -MAR00449,MAM01802m + MAM02914m --> MAM01690m + MAM01803m,ok,ok,ok,ok,N/A +MAR00483,MAM02914c + MAM03103m --> MAM01690c + MAM03102m,ok,ok,ok,ok,N/A MAR00604,MAM00240c + MAM01371c --> MAM01285c + MAM02039c + MAM02733c,ok,ok,ok,ok,N/A MAR00605,MAM00240c + MAM10007c --> MAM01597c + MAM02958c,ok,ok,ok,ok,N/A MAR00665,MAM02040c + MAM02958c --> MAM00240c + MAM02039c + MAM10005c,ok,ok,ok,ok,N/A @@ -8198,7 +8198,6 @@ MAR01078,MAM03578g <=> MAM03578c,only when going backwards,ok,ok,ok,N/A MAR01083,2 MAM01950g + MAM03584g --> MAM01856g + 2 MAM01948g + 2 MAM02039g,ok,ok,ok,ok,N/A MAR01118,MAM01950g + MAM03092g --> MAM01948g + MAM02039g + MAM03578g,ok,ok,ok,ok,N/A MAR01141,MAM01950g + MAM03095g --> MAM01948g + MAM02039g + MAM03577g,ok,ok,ok,ok,N/A -MAR01169,MAM01802m + MAM02914c --> MAM01690c + MAM01803m,ok,ok,ok,ok,N/A MAR01314,MAM00970c + MAM01371c + MAM02040c --> MAM00970e + MAM01285c + MAM02039c + MAM02751c,ok,ok,ok,MAR07738,N/A MAR01340,MAM01915g <=> MAM01884c,ok,ok,ok,ok,N/A MAR01348,MAM03586c <=> MAM03586g,only when going backwards,ok,ok,ok,N/A @@ -9365,7 +9364,6 @@ MAR07813,MAM01398r + MAM03109r --> MAM01397r + MAM03106r,ok,ok,ok,ok,N/A MAR07817,MAM01627e + MAM02630e --> MAM02039e + MAM02157e,ok,ok,ok,ok,N/A MAR07819,MAM03103e <=> MAM03103c,ok,ok,ok,ok,N/A MAR07821,MAM01642c --> MAM01642m,ok,ok,ok,ok,N/A -MAR08111,MAM01690m --> MAM01690c,ok,ok,ok,ok,N/A MAR08204,MAM01674e + MAM02040e --> MAM01334e + 2 MAM02039e + MAM02741e,ok,ok,ok,ok,N/A MAR08218,MAM01675r + MAM02039r + MAM02555r --> MAM01450r + MAM02554r,ok,ok,ok,ok,N/A MAR08274,MAM01371m + MAM01752m --> MAM01285m + MAM01747m,ok,ok,ok,ok,N/A diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index fdac8f39..e0a932e3 100644 --- a/data/testResults/model_qc_summary.md +++ b/data/testResults/model_qc_summary.md @@ -1,59 +1,59 @@ ## Model quality report -:warning: **6 pre-existing finding(s), no regressions vs `main`.** Non-blocking. +:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking. -_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md)._ +_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md)._ ### Model checks _Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report._ -| Check | Result | Δ vs `main` | | +| Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#duplicate-omap-keys) | 0 | new | :white_check_mark: | -| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: | -| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-with-no-metabolites) | 0 | new | :white_check_mark: | -| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | new | :white_check_mark: | -| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: | -| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-formula) | 0 | new | :white_check_mark: | -| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-charge) | 0 | new | :white_check_mark: | -| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | new | :white_check_mark: | -| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | new | :white_check_mark: | -| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-metabolites) | 0 | new | :white_check_mark: | -| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-genes) | 0 | new | :white_check_mark: | -| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#malformed-cross-references) | 0 | new | :white_check_mark: | -| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_annotation_issues.csv) | new | :warning: | +| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: | +| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: | +| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: | +| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: | +| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: | +| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: | +| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: | +| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: | +| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: | +| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: | +| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: | +| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: | +| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_annotation_issues.csv) | 0 | :warning: | ### MACAW and mass/charge balance -| Check | Result | Δ vs `main` | | +| Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -703 | :warning: | -| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -2 | :warning: | -| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: | -| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: | -| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_structure_consistency.csv) | new | :warning: | +| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | 0 | :warning: | +| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/macaw_results.csv) | 0 | :warning: | +| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: | +| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/balance_results.csv) | 0 | :warning: | +| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/qc_structure_consistency.csv) | 0 | :warning: | ### Model file and metabolic tasks | Check | Result | | | --- | ---: | :---: | -| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: | -| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: | -| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: | -| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: | -| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: | +| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: | +| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: | +| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: | +| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: | +| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: | -### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#memote) +### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#memote) -**Total score: 63.2%** (core subset)   +**Total score: 63.2%** (core subset)   0 | Section | Score | Δ vs base | | --- | ---: | ---: | -| consistency | 42.4% | | -| annotation_met | 73.0% | | -| annotation_rxn | 72.7% | | -| annotation_gene | 46.7% | | -| annotation_sbo | 81.7% | | +| consistency | 42.4% | 0 | +| annotation_met | 73.0% | 0 | +| annotation_rxn | 72.7% | 0 | +| annotation_gene | 46.7% | 0 | +| annotation_sbo | 81.7% | 0 |
Per-test scores @@ -89,11 +89,11 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
-**Full suite: 64.2%**   · _from the last_ `/run memote`. +**Full suite: 64.2%**   0 · _from the last_ `/run memote`. _The score above is the fast core subset. Comment_ `/run memote` _to run the full suite on this pull request; the score updates here when it finishes._ -### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#gene-essentiality-hart-2015) +### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-coupling/data/testResults/README.md#gene-essentiality-hart-2015) _Not run automatically (it takes hours). Comment_ `/run gene-essentiality` _to run it on this pull request; the result posts as its own comment._ diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5dc46667..5727b491 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -19996,13 +19996,6 @@ - formula: "C3H5O6P" - charge: -2 - metFrom: "HMRdatabase" - - !!omap - - id: "MAM01690m" - - name: "DHAP" - - compartment: "m" - - formula: "C3H5O6P" - - charge: -2 - - metFrom: "HMRdatabase" - !!omap - id: "MAM01690x" - name: "DHAP" @@ -70453,20 +70446,20 @@ - subsystem: "Arginine and proline metabolism" - confidence_score: 0 - !!omap - - id: "MAR08611" - - name: "L-proline:(acceptor) oxidoreductase" + - id: "MAR03838" + - name: "L-proline:ubiquinone oxidoreductase" - metabolites: !!omap - MAM00559m: 1 - - MAM01802m: -1 - - MAM01803m: 1 - MAM02039m: 1 - MAM02770m: -1 + - MAM03102m: 1 + - MAM03103m: -1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000100033 or ENSG00000250799" - rxnFrom: "HMRdatabase" - eccodes: "1.5.5.2" - - references: "PMID:18506409" + - references: "PMID:18506409;PMID:28990412" - subsystem: "Arginine and proline metabolism" - confidence_score: 0 - !!omap @@ -83461,7 +83454,7 @@ - MAM03103m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000016391 or ENSG00000100033 or ENSG00000102967 or ENSG00000105379 or ENSG00000115159 or ENSG00000137767 or ENSG00000140374 or ENSG00000171503 or ENSG00000250799" + - gene_reaction_rule: "ENSG00000105379 and ENSG00000140374 and ENSG00000171503" - rxnFrom: "HMRdatabase" - eccodes: "1.5.5.1" - references: "PMID:34428349" @@ -101768,20 +101761,20 @@ - subsystem: "Acylglycerides metabolism" - confidence_score: 0 - !!omap - - id: "MAR00449" - - name: "sn-Glycerol-3-phosphate:(acceptor) 2-oxidoreductase" + - id: "MAR00483" + - name: "sn-glycerol-3-phosphate:ubiquinone oxidoreductase" - metabolites: !!omap - - MAM01690m: 1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02914m: -1 + - MAM01690c: 1 + - MAM02914c: -1 + - MAM03102m: 1 + - MAM03103m: -1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000115159" - rxnFrom: "HMRdatabase" - eccodes: "1.1.5.3" - - references: "PMID:11955283;PMID:2115809;PMID:2923620;PMID:3338458;PMID:340460;PMID:8401296;PMID:8549872;PMID:8579375;PMID:9171333;PMID:9244403;PMID:9559543;PMID:7821823;PMID:8687421;PMID:8163052" - - subsystem: "Acylglycerides metabolism" + - references: "PMID:11955283;PMID:2115809;PMID:2923620;PMID:3338458;PMID:340460;PMID:8401296;PMID:8549872;PMID:8579375;PMID:9171333;PMID:9244403;PMID:9559543" + - subsystem: "Glycerophospholipid metabolism" - confidence_score: 0 - !!omap - id: "MAR00604" @@ -187812,22 +187805,6 @@ - references: "PMID:10386598" - subsystem: "Blood group biosynthesis" - confidence_score: 0 - - !!omap - - id: "MAR01169" - - name: "Glycerol-3-Phosphate Dehydrogenase (FAD), Mitochondrial" - - metabolites: !!omap - - MAM01690c: 1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02914c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115159" - - rxnFrom: "Recon3D" - - eccodes: "1.1.5.3" - - references: "PMID:11955283;PMID:2115809;PMID:2923620;PMID:3338458;PMID:340460;PMID:8401296;PMID:8549872;PMID:8579375;PMID:9171333;PMID:9244403;PMID:9559543;PMID:11385633" - - subsystem: "Glycolysis / Gluconeogenesis" - - confidence_score: 0 - !!omap - id: "MAR01314" - name: "GABA Secretion via Secretory Vesicle (ATP Driven)" @@ -205599,17 +205576,6 @@ - references: "PMID:16816105;PMID:17403938" - subsystem: "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR08111" - - name: "Transport of Dihydroxyacetone Phosphate into Cytosol" - - metabolites: !!omap - - MAM01690c: 1 - - MAM01690m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - rxnFrom: "Recon3D" - - subsystem: "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR08204" - name: "pyrophasphatase (dephospho-CoA, extracellular)" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index be4644ca..4b201454 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -2827,7 +2827,6 @@ MAM01689l MAM01689 crvnc C06429 HMDB0002183 CHEBI:77016 445580 LMFA01030185 CE03 MAM01689r MAM01689 crvnc C06429 HMDB0002183 CHEBI:77016 445580 LMFA01030185 CE0328 crvnc MNXM7161 CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCC(=O)[O-] InChI=1S/C22H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22(23)24/h3-4,6-7,9-10,12-13,15-16,18-19H,2,5,8,11,14,17,20-21H2,1H3,(H,23,24)/p-1/b4-3-,7-6-,10-9-,13-12-,16-15-,19-18- cpd03852 m01689r m01689r MAM01689e MAM01689 crvnc C06429 HMDB0002183 CHEBI:77016 445580 LMFA01030185 CE0328 crvnc MNXM7161 CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCC(=O)[O-] InChI=1S/C22H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22(23)24/h3-4,6-7,9-10,12-13,15-16,18-19H,2,5,8,11,14,17,20-21H2,1H3,(H,23,24)/p-1/b4-3-,7-6-,10-9-,13-12-,16-15-,19-18- cpd03852 m01689s m01689s MAM01690c MAM01690 dhap C00111 HMDB0001473 CHEBI:16108 668 HC00109 dhap MNXM77 O=C(CO)COP(=O)([O-])[O-] InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2 cpd00095 m01690c m01690c -MAM01690m MAM01690 dhap C00111 HMDB0001473 CHEBI:16108 668 HC00109 dhap MNXM77 O=C(CO)COP(=O)([O-])[O-] InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2 cpd00095 m01690m m01690m MAM01690x MAM01690 dhap C00111 HMDB0001473 CHEBI:16108 668 HC00109 dhap MNXM77 O=C(CO)COP(=O)([O-])[O-] InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2 cpd00095 m01690p m01690p MAM01690e MAM01690 dhap C00111 HMDB0001473 CHEBI:16108 668 HC00109 dhap MNXM77 O=C(CO)COP(=O)([O-])[O-] InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2 cpd00095 m01690s m01690s MAM01691c MAM01691 C11149 CHEBI:28240 LMFA01090070 M01691 MNXM5126 O=C([O-])C(Cl)Cl InChI=1S/C2H2Cl2O2/c3-1(4)2(5)6/h1H,(H,5,6)/p-1 cpd08027 m01691c m01691c diff --git a/model/reactions.tsv b/model/reactions.tsv index 74283fb5..61427fe3 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -632,7 +632,7 @@ MAR08607 UNK2 UNK2 MNXR105128 HMR_8607 RCR10315 0 HMR_8607 MAR08608 R02894 DRIBt HMR_8608 MNXR107807 HMR_8608 RCR14308 0 RHEA:78259 HMR_8608 MAR08609 R01251 P5CRm P5CRm MNXR102302 HMR_8609 RCR10244 0 RHEA:14109 RHEA:14109 HMR_8609 MAR08610 R10507 PROD2 PROD2 MNXR192607 HMR_8610 RCR10316 0 HMR_8610 -MAR08611 R10507 PROD2m r1453 PROD2m MNXR192607 HMR_8611;HMR_3838 RCR11294;RCR14286 0 HMR_8611;HMR_3838;MAR03838 +MAR03838 R10507 PROD2m r1453 PROD2m MNXR103187 HMR_3838 RCR14286 0 HMR_3838;HMR_8611;MAR08611 MAR04285 R00713 SSALx R00713C r0178 r0178 MNXR104540 HMR_4285 RCR11295 0 RHEA:13218 RHEA:13217 HMR_4285 MAR00457 R01514 GLYCK R01514C r0339 r0339 MNXR100328 HMR_0457 RCR11296 0 RHEA:23517 RHEA:23516 HMR_0457 MAR00460 R01514 GLYCK R01514C r0340 r0340 MNXR100328 HMR_0460 RCR11297 0 RHEA:23517 RHEA:23516 HMR_0460 @@ -2474,7 +2474,7 @@ MAR00001 R-HSA-174757 HMR_0001 HMR_0001 RCR30273 0 HMR_0001 MAR00002 R02250 HMR_0002 HMR_0002 RCR30274 0 HMR_0002 MAR00003 R02687 HMR_0003 HMR_0003 RCR30275 0 HMR_0003 MAR00005 R01351 HMR_0005 HMR_0005 RCR12493 0 RHEA:34019 HMR_0005 -MAR00449 R00848;R00849 G3PD r0205 R-HSA-188467 GLYC3PFADm;r0205 MNXR192664 HMR_0449;HMR_0483 RCR12494;RCR21050 0 RHEA:31283 RHEA:31283;RHEA:18977 HMR_0449;HMR_0483 +MAR00483 R00848;R00849 G3PD2m R00848C G3PD2m MNXR99878 HMR_0483 RCR21050 0 RHEA:18977 HMR_0449;HMR_0483;MAR00449;MAR01169 MAR00604 R02240 DAGK_hs DAGK_hs HMR_0604 RCR14512 0 RHEA:10272 HMR_0604 MAR00605 R02251 r1223 HMR_0605 HMR_0605 RCR12495 0 RHEA:10868 HMR_0605 MAR00665 R02250 r1224 HMR_0665 HMR_0665 RCR14513 0 HMR_0665 @@ -8197,8 +8197,7 @@ MAR01078 FUCFUCGALACGLCGALGLUSIDEtg FUCFUCGALACGLCGALGLUSIDEtg MNXR99694 MAR01083 FUT18g FUT18g MNXR99731 0 FUT18g MAR01118 FUT34g FUT34g MNXR99739 0 FUT34g MAR01141 FUT93g FUT93g MNXR99751 0 FUT93g -MAR01169 R00849;R00848 G3PD2m R00848C r0205 G3PD2m;r0205;HMR_0482 MNXR99878;MNXR106713;MNXR192664 HMR_0483;HMR_0482 RCR21050;RCR14578 0 RHEA:31283 RHEA:18977 G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483 -MAR01314 GABAVESSEC GABAVESSEC MNXR137724 0 GABAVESSEC +MAR01314 GABAVESSEC GABAVESSEC MNXR99916 0 GABAVESSEC MAR01340 GALFUCGALACGLCGAL14ACGLCGALGLUSIDEtg GALFUCGALACGLCGAL14ACGLCGALGLUSIDEtg MNXR99968 0 GALFUCGALACGLCGAL14ACGLCGALGLUSIDEtg MAR01348 GALGLUSIDEtg GALGLUSIDEtg MNXR99974 0 GALGLUSIDEtg MAR01349 GALGLUSIDEtl GALGLUSIDEtl MNXR99974 0 GALGLUSIDEtl @@ -9365,7 +9364,6 @@ MAR07813 BIDGLCURr BIDGLCURr MNXR154864 0 BIDGLCURr MAR07817 R02467 CYSAMOe CYSAMOe MNXR96988 0 RHEA:14410 RHEA:14409 CYSAMOe MAR07819 Coqe Coqe MNXR97066 0 Coqe MAR07821 DATPtm_cho DATPtm MNXR97176 0 DATPtm -MAR08111 DHAPtm DHAPtc MNXR97366 0 DHAPtc MAR08204 DPCOAPPe DPCOAPPe MNXR97763 0 DPCOAPPe MAR08218 R01457 DSREDUCr DSREDUCr MNXR97801 0 RHEA:36391 DSREDUCr MAR08274 R02094 DTMPKm DTMPKm MNXR97804 0 RHEA:13518 RHEA:13517 DTMPKm