From d17703cdcda1d2d70d8a0c77b89a0a8cd62ca4f6 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Fri, 6 Dec 2024 12:31:59 +0800 Subject: [PATCH 1/9] Fix: GPR curation for Starch and sucrose metabolism --- model/Human-GEM.yml | 23 ++++++++++------------- model/genes.tsv | 1 - 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7a41c271..6ad11be3 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -68303,7 +68303,7 @@ - MAM02450e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000092529 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335" + - gene_reaction_rule: "ENSG00000171298 or ENSG00000214013 or ENSG00000257335" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.20" @@ -68340,7 +68340,7 @@ - MAM03039e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000118094 or ENSG00000142102" + - gene_reaction_rule: "ENSG00000118094" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.28" @@ -68500,7 +68500,7 @@ - MAM02448c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -68572,7 +68572,7 @@ - MAM02447c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -68608,7 +68608,7 @@ - MAM02449c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -68644,7 +68644,7 @@ - MAM02451c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -68680,7 +68680,7 @@ - MAM02452c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -68770,7 +68770,7 @@ - MAM02452c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -68787,7 +68787,7 @@ - MAM02450c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.1" @@ -218065,7 +218065,7 @@ - MAM03622e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000021488 and ENSG00000138079) or ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" + - gene_reaction_rule: "ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "3.2.1.1" @@ -305846,9 +305846,6 @@ - !!omap - id: "ENSG00000092295" - name: "TGM1" - - !!omap - - id: "ENSG00000092529" - - name: "CAPN3" - !!omap - id: "ENSG00000092621" - name: "PHGDH" diff --git a/model/genes.tsv b/model/genes.tsv index 763bde13..375d8282 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -389,7 +389,6 @@ ENSG00000092068 "ENST00000339733;ENST00000316902;ENST00000397310;ENST00000422941 ENSG00000092098 "ENST00000560875;ENST00000559308;ENST00000558634;ENST00000557878;ENST00000559533;ENST00000557991;ENST00000559438;ENST00000560071;ENST00000559275;ENST00000324103;ENST00000559882;ENST00000559260;ENST00000560342;ENST00000558907;ENST00000560787;ENST00000559583;ENST00000491351;ENST00000559071;ENST00000560754;ENST00000558452;ENST00000559449;ENST00000483895;ENST00000559719;ENST00000559491;ENST00000560631" "ENSP00000454032;ENSP00000453471;ENSP00000454048;ENSP00000453423;ENSP00000453948;ENSP00000453574;ENSP00000315112;ENSP00000453645;ENSP00000453601;ENSP00000452972;ENSP00000499015;ENSP00000453595;ENSP00000454140;ENSP00000453672;ENSP00000452820" Q96EP0 RNF31 55072 ring finger protein 31 "FLJ10111;FLJ23501;HOIP;Paul;ZIBRA" Cytosol "SwissProt;CellAtlas" ENSG00000092148 "ENST00000554882;ENST00000399332;ENST00000555843;ENST00000611816;ENST00000553700;ENST00000556281;ENST00000557695;ENST00000555311;ENST00000553957;ENST00000557321;ENST00000554027;ENST00000555915;ENST00000556004;ENST00000557369;ENST00000554850;ENST00000556224;ENST00000554471;ENST00000553616;ENST00000556474" "ENSP00000451260;ENSP00000382269;ENSP00000484981;ENSP00000450697;ENSP00000451860;ENSP00000450920;ENSP00000452233;ENSP00000452015;ENSP00000479695" Q9ULT8 HECTD1 25831 HECT domain E3 ubiquitin protein ligase 1 KIAA1131 Nucleus CellAtlas ENSG00000092295 "ENST00000206765;ENST00000544573;ENST00000559669;ENST00000559136;ENST00000558074;ENST00000560443;ENST00000560478;ENST00000560226;ENST00000561067" "ENSP00000206765;ENSP00000439446;ENSP00000453701;ENSP00000453337;ENSP00000453840;ENSP00000452822;ENSP00000453234;ENSP00000454070;ENSP00000452690" P22735 TGM1 7051 transglutaminase 1 "ICR2;LI;LI1;TGASE;TGK" Cytosol DeepLoc2 -ENSG00000092529 "ENST00000349748;ENST00000397163;ENST00000357568;ENST00000638141;ENST00000673705;ENST00000673658;ENST00000673813;ENST00000397200;ENST00000569827;ENST00000673646;ENST00000567071;ENST00000673854;ENST00000674093;ENST00000569136;ENST00000673936;ENST00000673890;ENST00000674149;ENST00000673771;ENST00000337571;ENST00000673743;ENST00000673939;ENST00000674146;ENST00000674119;ENST00000674064;ENST00000673692;ENST00000565173;ENST00000674052;ENST00000561817;ENST00000674018;ENST00000397204;ENST00000673886;ENST00000674139;ENST00000673851;ENST00000673839;ENST00000673978;ENST00000673987;ENST00000673928;ENST00000674041;ENST00000565559;ENST00000673750;ENST00000674011;ENST00000674135;ENST00000674012;ENST00000565274;ENST00000674140;ENST00000564503;ENST00000673774;ENST00000673950;ENST00000466222;ENST00000673687;ENST00000674027;ENST00000674130;ENST00000562199;ENST00000673893;ENST00000673684;ENST00000568153;ENST00000567817;ENST00000356316;ENST00000318023" "ENSP00000183936;ENSP00000380349;ENSP00000350181;ENSP00000501021;ENSP00000380384;ENSP00000454379;ENSP00000501007;ENSP00000456607;ENSP00000501303;ENSP00000455254;ENSP00000501189;ENSP00000501293;ENSP00000501112;ENSP00000501023;ENSP00000336840;ENSP00000500989;ENSP00000501129;ENSP00000501175;ENSP00000501217;ENSP00000501138;ENSP00000501057;ENSP00000456575;ENSP00000501271;ENSP00000380387;ENSP00000501155;ENSP00000501054;ENSP00000501142;ENSP00000501188;ENSP00000500976;ENSP00000501231;ENSP00000501099;ENSP00000500956;ENSP00000457878;ENSP00000501173;ENSP00000501171;ENSP00000501178;ENSP00000457759;ENSP00000457898;ENSP00000501034;ENSP00000500987;ENSP00000454937;ENSP00000456514;ENSP00000348667;ENSP00000326281" P20807 CAPN3 825 calpain 3 "CANP3;LGMD2;LGMD2A;nCL-1;p94" "Cytosol;Nucleus" SwissProt ENSG00000092621 "ENST00000641597;ENST00000493622;ENST00000641720;ENST00000642041;ENST00000641947;ENST00000641213;ENST00000641074;ENST00000496756;ENST00000641115;ENST00000642021;ENST00000641491;ENST00000369409;ENST00000641023;ENST00000641513;ENST00000641573;ENST00000641587;ENST00000641570;ENST00000641891;ENST00000641375;ENST00000462324;ENST00000641371;ENST00000641272;ENST00000641247;ENST00000641756;ENST00000641711;ENST00000641927;ENST00000641314;ENST00000369407;ENST00000641811;ENST00000641847;ENST00000641455;ENST00000469443;ENST00000641939;ENST00000482968" "ENSP00000493382;ENSP00000493433;ENSP00000492948;ENSP00000493415;ENSP00000492994;ENSP00000493079;ENSP00000493446;ENSP00000493264;ENSP00000493187;ENSP00000358417;ENSP00000493175;ENSP00000493398;ENSP00000493453;ENSP00000493213;ENSP00000493288;ENSP00000493089;ENSP00000493305;ENSP00000493432;ENSP00000492955;ENSP00000493147;ENSP00000493296" O43175 PHGDH 26227 phosphoglycerate dehydrogenase "PDG;PGDH;SERA" "Cytosol;Nucleus" CellAtlas ENSG00000092964 "ENST00000521913;ENST00000493789;ENST00000311151;ENST00000523027;ENST00000523690;ENST00000523093;ENST00000521983;ENST00000474808" "ENSP00000427985;ENSP00000427954;ENSP00000309539;ENSP00000431117" Q16555 DPYSL2 1808 dihydropyrimidinase like 2 "CRMP2;DHPRP2;DRP-2;DRP2" Cytosol "SwissProt;CellAtlas" ENSG00000093000 "ENST00000347635;ENST00000407019;ENST00000424634;ENST00000417702;ENST00000497960;ENST00000461437;ENST00000434760;ENST00000430547;ENST00000484186;ENST00000445721;ENST00000493456;ENST00000396096;ENST00000461194;ENST00000432340;ENST00000419387;ENST00000422489;ENST00000486184;ENST00000491860;ENST00000469163" "ENSP00000345895;ENSP00000385555;ENSP00000415062;ENSP00000394450;ENSP00000388426;ENSP00000397960;ENSP00000398297;ENSP00000379403;ENSP00000400465;ENSP00000391987;ENSP00000416264" Q9UKX7 NUP50 10762 nucleoporin 50 NPAP60L Nucleus "SwissProt;CellAtlas" From 548d5fa5208b57fc58a435558a808a1bddc2b0d7 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Fri, 6 Dec 2024 04:58:02 +0000 Subject: [PATCH 2/9] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index adfaae5b..39140d5d 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. From 8a855e87d7fb17e5a7b760da3038430f9550c5ce Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Sat, 7 Dec 2024 11:03:57 +0800 Subject: [PATCH 3/9] Fix: GPR curation for subsystems related with amino acid --- model/Human-GEM.yml | 21 +++++++++------------ model/genes.tsv | 1 - 2 files changed, 9 insertions(+), 13 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7a41c271..278e3b90 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -77405,7 +77405,7 @@ - MAM02943m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000134333" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.16" @@ -80744,7 +80744,7 @@ - MAM03124c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006695 or ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665" + - gene_reaction_rule: "ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.5.1.-" @@ -85711,7 +85711,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000181652 or ENSG00000184470 or ENSG00000197763 or ENSG00000198431" + - gene_reaction_rule: "ENSG00000184470 or ENSG00000197763 or ENSG00000198431" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.8.1.9" @@ -86410,7 +86410,7 @@ - MAM02041e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116157 or ENSG00000117450 or ENSG00000117592 or ENSG00000126432 or ENSG00000164294 or ENSG00000165672 or ENSG00000167468 or ENSG00000167815 or ENSG00000176153 or ENSG00000198704 or ENSG00000211445 or ENSG00000224586 or ENSG00000233276" + - gene_reaction_rule: "ENSG00000116157 or ENSG00000117450 or ENSG00000117592 or ENSG00000126432 or ENSG00000164294 or ENSG00000167468 or ENSG00000167815 or ENSG00000176153 or ENSG00000198704 or ENSG00000211445 or ENSG00000224586 or ENSG00000233276" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.11.1.9;1.11.1.15" @@ -86668,7 +86668,7 @@ - MAM02039c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000128683 or ENSG00000136750" + - gene_reaction_rule: "ENSG00000136750" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.11;4.1.1.15" @@ -86882,7 +86882,7 @@ - MAM02885c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000138801 or ENSG00000198682" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.7.4" @@ -88067,7 +88067,7 @@ - MAM02527c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111261 or ENSG00000133048 or ENSG00000133063 or ENSG00000134216" + - gene_reaction_rule: "ENSG00000111261 or ENSG00000133063 or ENSG00000134216" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.14" @@ -93247,7 +93247,7 @@ - MAM03135c: 28 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165996 or ENSG00000206527" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.134" @@ -218356,7 +218356,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.5.1.12" @@ -311948,9 +311948,6 @@ - !!omap - id: "ENSG00000181555" - name: "SETD2" - - !!omap - - id: "ENSG00000181652" - - name: "ATG9B" - !!omap - id: "ENSG00000181788" - name: "SIAH2" diff --git a/model/genes.tsv b/model/genes.tsv index 763bde13..1178753a 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2407,7 +2407,6 @@ ENSG00000181192 "ENST00000263035;ENST00000437298;ENST00000465617;ENST00000415935 ENSG00000181222 "ENST00000674977;ENST00000617998;ENST00000572844;ENST00000576952;ENST00000575547;ENST00000576114;ENST00000576718;ENST00000574158;ENST00000573603;ENST00000576553" ENSP00000502190 A0A6Q8PGB0 POLR2A 5430 RNA polymerase II subunit A "POLR2;POLRA;RPB1" "Cytosol;Nucleus" CellAtlas ENSG00000181523 "ENST00000575484;ENST00000571156;ENST00000572257;ENST00000326317;ENST00000575282;ENST00000573150;ENST00000576856;ENST00000570923;ENST00000576941;ENST00000574505;ENST00000572208;ENST00000571051;ENST00000576707;ENST00000570427;ENST00000571675;ENST00000575188;ENST00000571075" "ENSP00000461827;ENSP00000314606;ENSP00000459280;ENSP00000460720;ENSP00000458200;ENSP00000461160;ENSP00000459708;ENSP00000461128;ENSP00000459765" P51688 SGSH 6448 N-sulfoglucosamine sulfohydrolase "HSS;MPS3A;SFMD" Lysosome SwissProt ENSG00000181555 "ENST00000431180;ENST00000330022;ENST00000409792;ENST00000445387;ENST00000479832;ENST00000492397;ENST00000638947;ENST00000484689;ENST00000412450" "ENSP00000388349;ENSP00000332415;ENSP00000386759;ENSP00000411901;ENSP00000491413;ENSP00000416401" Q9BYW2 SETD2 29072 SET domain containing 2, histone lysine methyltransferase "FLJ23184;HIF-1;HYPB;KIAA1732;KMT3A" "Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000181652 "ENST00000498521;ENST00000605952;ENST00000639579;ENST00000617967;ENST00000404733;ENST00000476282;ENST00000471797;ENST00000611177;ENST00000469530;ENST00000473409;ENST00000473134;ENST00000466157" "ENSP00000475737;ENSP00000491504;ENSP00000479879" Q674R7 ATG9B 285973 autophagy related 9B "APG9L2;FLJ14885;NOS3AS;SONE" Cytosol SwissProt ENSG00000181788 "ENST00000312960;ENST00000482706;ENST00000472885" "ENSP00000322457;ENSP00000417619" O43255 SIAH2 6478 siah E3 ubiquitin protein ligase 2 "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000181789 "ENST00000314797;ENST00000513965;ENST00000515725;ENST00000504350;ENST00000509208;ENST00000504547;ENST00000513410;ENST00000509889;ENST00000514478;ENST00000512034" "ENSP00000325002;ENSP00000426457;ENSP00000422478;ENSP00000420916" Q9Y678 COPG1 22820 COPI coat complex subunit gamma 1 COPG "Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000181804 "ENST00000316549;ENST00000483124;ENST00000474727;ENST00000474151;ENST00000498717" "ENSP00000320246;ENSP00000419090;ENSP00000418627" Q8IVB4 SLC9A9 285195 solute carrier family 9 member A9 "FLJ35613;NHE9" "Cell membrane;Lysosome" DeepLoc2 From bc79aec5d1921ad51098a12fc2a0b80d02d7e86c Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Sat, 7 Dec 2024 03:19:20 +0000 Subject: [PATCH 4/9] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index adfaae5b..c83a2491 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. From de496404b4c87f2bb75d14fe84839e9e8f1ab287 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Sat, 7 Dec 2024 14:26:57 +0800 Subject: [PATCH 5/9] Fix: GPR curation for Sulfur metabolism --- model/Human-GEM.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7a41c271..89c2a606 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -93535,7 +93535,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000104331 or ENSG00000162813" + - gene_reaction_rule: "ENSG00000162813" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.7" @@ -93611,7 +93611,7 @@ - MAM02877c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000132746 or ENSG00000184254" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -140094,7 +140094,7 @@ - MAM02946l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000106304 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614" + - gene_reaction_rule: "ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.35;3.2.1.52" @@ -140337,7 +140337,7 @@ - MAM02946l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386" + - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5" @@ -140412,7 +140412,7 @@ - MAM02946l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386" + - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5" @@ -140508,7 +140508,7 @@ - MAM02946l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386" + - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5" @@ -140602,7 +140602,7 @@ - MAM02946l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386" + - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5" @@ -140735,7 +140735,7 @@ - MAM02946l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386" + - gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5" @@ -142090,7 +142090,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" From 05cd3f4821d60ee58d778f07610a79e988a00e81 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Sat, 7 Dec 2024 06:58:30 +0000 Subject: [PATCH 6/9] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index adfaae5b..1e25d652 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #913** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #937** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. From f9d560dbf290e630a6801958f4d1b7f47d0184bb Mon Sep 17 00:00:00 2001 From: feiranl Date: Mon, 16 Dec 2024 11:44:51 +0000 Subject: [PATCH 7/9] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 1e25d652..c83a2491 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #937** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. From 30975e88bf12e4a8ff8d7dd5dfff151b76307aa5 Mon Sep 17 00:00:00 2001 From: feiranl Date: Mon, 16 Dec 2024 11:53:46 +0000 Subject: [PATCH 8/9] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index c83a2491..39140d5d 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. From ccc8b29ba9b9ce9a09cb15ed09b04c996fc4c851 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer <33460176+Devlin-Moyer@users.noreply.github.com> Date: Mon, 16 Dec 2024 19:16:15 -0500 Subject: [PATCH 9/9] Fix Duplicate Stearoyl-CoA Beta-Oxidation Reactions (#820) * fix: removed MAR00776 and MAR00778 from YAML file * feat: added appropriate refs for MAR03115-8 since refs from MAR00776 weren't appropriate * chore: merged annotations for MAR00776 with those for MAR03115-8 in reactions.tsv and moved MAR00776 to deprecatedReactions.tsv * chore: merged annotations for MAR00778 with those for MAR03116-MAR03146 in reactions.tsv and moved MAR00778 to deprecatedReactions.tsv * fix: indentation error in YAML file * fix: removed incorrect MetaNetX IDs for MAR03117 and MAR03118 * chore: add macaw test result * chore: add macaw test result --------- Co-authored-by: Eduard Kerkhoven Co-authored-by: Devlin-Moyer Co-authored-by: edkerk --- .../deprecatedReactions.tsv | 2 + data/testResults/README.md | 2 +- data/testResults/macaw_results.csv | 2 - model/Human-GEM.yml | 56 ++----------------- model/reactions.tsv | 42 +++++++------- 5 files changed, 27 insertions(+), 77 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 69cfefad..39779b48 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -300,3 +300,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745" "MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747" "MAR07799" "" "ATPasel" "" "" "" "" "MNXR96136" "HMR_7799" "RCR20334" "" 0 "" "" "HMR_7799" +"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180" +"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m" diff --git a/data/testResults/README.md b/data/testResults/README.md index 39140d5d..5a49a7d3 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #820** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index aa73eeed..112e0ccf 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -8250,9 +8250,7 @@ MAR00759,4 MAM01597x + 4 MAM01802x + 4 MAM02040x + 4 MAM02552x + MAM02678x --> 4 MAR00764,MAM00051m + 4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00772,4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m + MAM02677m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00774,7 MAM01597m + 7 MAM01802m + 7 MAM02040m + MAM02101m + 7 MAM02552m --> 7 MAM01261m + 7 MAM01803m + 7 MAM02039m + 7 MAM02553m + MAM02774m,ok,ok,ok,ok,N/A -MAR00776,MAM01597m + MAM01802m + MAM02040m + MAM02552m + MAM02941m --> MAM01261m + MAM01803m + MAM02039m + MAM02553m + MAM02678m,ok,ok,ok,ok,N/A MAR00777,MAM01597x + MAM01802x + MAM02040x + MAM02552x + MAM02941x --> MAM01261x + MAM01803x + MAM02039x + MAM02553x + MAM02678x,ok,ok,ok,ok,N/A -MAR00778,MAM00057m + 5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00780,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM03791m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00784,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM02647m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00785,5 MAM01597m + 3 MAM01802m + 5 MAM02040m + MAM02391m + 5 MAM02552m --> 5 MAM01261m + 3 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5f1cbb0c..568b3f1d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -118350,7 +118350,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.3.8.7;1.3.8.8;1.3.8.9;1.3.99.-" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118367,7 +118367,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.17" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118386,7 +118386,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.35;1.1.1.211" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118404,7 +118404,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.16;1.1.1.211" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -221482,30 +221482,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR00776" - - name: "Beta Oxidation of Long Chain Fatty Acid" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM02678m: 1 - - MAM02941m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "1.3.99.3" - - references: "PMID:2565344;PMID:3035565" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR00777" - name: "Beta Oxidation of Long Chain Fatty Acid" @@ -221530,30 +221506,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR00778" - - name: "Beta Oxidation Fatty Acid" - - metabolites: !!omap - - MAM00057m: -1 - - MAM01261m: 5 - - MAM01597m: -5 - - MAM01802m: -4 - - MAM01803m: 4 - - MAM02039m: 5 - - MAM02040m: -5 - - MAM02552m: -5 - - MAM02553m: 5 - - MAM02644m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "4.2.1.74" - - references: "" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR00780" - name: "Beta Oxidation Fatty Acid" diff --git a/model/reactions.tsv b/model/reactions.tsv index 1a9770d5..4fa8c7c9 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2624,26 +2624,26 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03112" "" "" "" "" "" "HMR_3112" "" "HMR_3112" "RCR12626" "" 0 "" "" "HMR_3112" "MAR03113" "" "" "" "" "" "HMR_3113" "" "HMR_3113" "RCR12627" "" 0 "" "" "HMR_3113" "MAR03114" "" "" "" "" "" "HMR_3114" "" "HMR_3114" "RCR12628" "" 0 "" "" "HMR_3114" -"MAR03115" "" "" "" "" "" "HMR_3115" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115" -"MAR03116" "R07760" "" "" "" "" "HMR_3116" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116" -"MAR03117" "" "" "" "" "" "HMR_3117" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117" -"MAR03118" "" "" "" "" "" "HMR_3118" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118" -"MAR03121" "R01279" "r0310" "" "" "R-HSA-77299" "HMR_3121;r0310" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035" -"MAR03122" "R04738" "" "R04738X" "r0716" "" "r0716" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122" -"MAR03123" "R04737" "" "R04737X" "r0714" "" "r0714" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123" -"MAR03125" "R03991" "" "R03991X" "r0653" "" "r0653" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125" -"MAR03128" "R03990" "r1449" "" "" "R-HSA-77274" "HMR_3128;r1449" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370" -"MAR03129" "R04740" "" "R04740X" "r0720" "" "r0720" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129" -"MAR03130" "R04739" "" "R04739X" "r0718" "" "r0718" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130" -"MAR03132" "R03858" "" "R03858X" "r0639" "" "r0639" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132" -"MAR03135" "R03857" "r1447" "" "" "R-HSA-77263" "HMR_3135;r1447" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367" -"MAR03136" "R04170" "r1446" "R04170X" "r0660" "" "r0660;r1446" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366" -"MAR03137" "R04741" "" "R04741X" "r0722" "" "r0722" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137" -"MAR03139" "R04742" "" "R04742X" "r0724" "" "r0724" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139" -"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024" -"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" -"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" -"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" +"MAR03115" "" "FAOXC180" "" "" "" "HMR_3115;FAOXC180" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115;FAOXC180;MAR00776" +"MAR03116" "R07760" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3116;FAOXC180;FAOXC1811601m" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03117" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3117;FAOXC180;FAOXC1811601m" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03118" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3118;FAOXC180;FAOXC1811601m" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03121" "R01279" "r0310;FAOXC1811601m" "" "" "R-HSA-77299" "HMR_3121;r0310;FAOXC1811601m" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035;FAOXC1811601m;MAR00778" +"MAR03122" "R04738" "FAOXC1811601m" "R04738X" "r0716" "" "r0716;FAOXC1811601m" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122;FAOXC1811601m;MAR00778" +"MAR03123" "R04737" "FAOXC1811601m" "R04737X" "r0714" "" "r0714;FAOXC1811601m" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123;FAOXC1811601m;MAR00778" +"MAR03125" "R03991" "FAOXC1811601m" "R03991X" "r0653" "" "r0653;FAOXC1811601m" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125;FAOXC1811601m;MAR00778" +"MAR03128" "R03990" "r1449;FAOXC1811601m" "" "" "R-HSA-77274" "HMR_3128;r1449;FAOXC1811601m" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370;FAOXC1811601m;MAR00778" +"MAR03129" "R04740" "FAOXC1811601m" "R04740X" "r0720" "" "r0720;FAOXC1811601m" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129;FAOXC1811601m;MAR00778" +"MAR03130" "R04739" "FAOXC1811601m" "R04739X" "r0718" "" "r0718;FAOXC1811601m" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130;FAOXC1811601m;MAR00778" +"MAR03132" "R03858" "FAOXC1811601m" "R03858X" "r0639" "" "r0639;FAOXC1811601m" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132;FAOXC1811601m;MAR00778" +"MAR03135" "R03857" "r1447;FAOXC1811601m" "" "" "R-HSA-77263" "HMR_3135;r1447;FAOXC1811601m" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367;FAOXC1811601m;MAR00778" +"MAR03136" "R04170" "r1446;FAOXC1811601m" "R04170X" "r0660" "" "r0660;r1446;FAOXC1811601m" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366;FAOXC1811601m;MAR00778" +"MAR03137" "R04741" "FAOXC1811601m" "R04741X" "r0722" "" "r0722;FAOXC1811601m" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137;FAOXC1811601m;MAR00778" +"MAR03139" "R04742" "FAOXC1811601m" "R04742X" "r0724" "" "r0724;FAOXC1811601m" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139;FAOXC1811601m;MAR00778" +"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m;FAOXC1811601m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m;FAOXC1811601m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" "MAR03149" "R03777" "r1448;FAOXC8C6m;FAOXC80" "" "" "R-HSA-77338" "HMR_3149;r1448;FAOXC6C8m;FAOXC80;HMR_3422" "MNXR95304" "HMR_3149;HMR_3422" "RCR12649;RCR12667" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03150" "R04746" "FAOXC8C6m;FAOXC80" "R04746M" "r0731" "" "r0731;FAOXC8C6m;FAOXC80;HMR_3422" "MNXR97888" "HMR_3150;HMR_3422" "RCR12650;RCR12667" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03151" "R04745" "FAOXC8C6m;FAOXC80" "R04745M" "r0730" "" "r0730;FAOXC8C6m;FAOXC80;HMR_3422" "MNXR100544" "HMR_3151;HMR_3422" "RCR12651;RCR12667" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" @@ -8249,9 +8249,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00764" "" "FAOXC161802m" "" "" "" "FAOXC161802m" "MNXR99301" "" "" "" 0 "" "" "FAOXC161802m" "MAR00772" "" "FAOXC16180m" "" "" "" "FAOXC16180m" "MNXR99302" "" "" "" 0 "" "" "FAOXC16180m" "MAR00774" "" "FAOXC170m" "" "" "" "FAOXC170m" "MNXR99312" "" "" "" 0 "" "" "FAOXC170m" -"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180" "MAR00777" "" "FAOXC180x" "" "" "" "FAOXC180x" "MNXR99314" "" "" "" 0 "" "" "FAOXC180x" -"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m" "MAR00780" "" "FAOXC1811602m" "" "" "" "FAOXC1811602m" "MNXR99316" "" "" "" 0 "" "" "FAOXC1811602m" "MAR00784" "" "FAOXC1811603m" "" "" "" "FAOXC1811603m" "MNXR99317" "" "" "" 0 "" "" "FAOXC1811603m" "MAR00785" "" "FAOXC182806m" "" "" "" "FAOXC182806m" "MNXR99321" "" "" "" 0 "" "" "FAOXC182806m"