From fd91d7f0ce3b4b42c64df98a811bc7e36e2b013c Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 19:49:23 -0500 Subject: [PATCH 1/6] fix: GPRs and references for MAR01801 and MAR01808 --- model/Human-GEM.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..b511bf68 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -194906,10 +194906,10 @@ - MAM03103c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000198431" + - gene_reaction_rule: "ENSG00000159228 or ENSG00000181019" - rxnFrom: "Recon3D" - eccodes: "1.8.1.9" - - references: "PMID:12435734;PMID:8577704;PMID:8999974" + - references: "PMID:12435734;PMID:7005231;PMID:8577704;PMID:8999974;PMID:16569397" - subsystem: - "Miscellaneous" - confidence_score: 0 @@ -194924,10 +194924,10 @@ - MAM03103c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000198431" + - gene_reaction_rule: "ENSG00000181019 or ENSG00000159348 or ENSG00000166394 or ENSG00000100243 or ENSG00000065615 or ENSG00000215883" - rxnFrom: "Recon3D" - eccodes: "1.8.1.9" - - references: "PMID:12435734;PMID:8577704;PMID:8999974" + - references: "PMID:12435734;PMID:8577704;PMID:8999974;PMID:16569397;PMID:9271353" - subsystem: - "Miscellaneous" - confidence_score: 0 From 29bdc6c98010b6de61a9e1723dbb89b02c1d24e7 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 19:57:06 -0500 Subject: [PATCH 2/6] fix: replace ubiquinol with NADPH and update GPR accordingly for MAR03047 --- model/Human-GEM.yml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b511bf68..92ca9829 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -199358,15 +199358,17 @@ - !!omap - id: "MAR03047" - metabolites: !!omap - - MAM01328c: -1 - - MAM01329c: 1 - - MAM03102c: 1 - - MAM03103c: -1 - - lower_bound: -1000 + - MAM01328c: 1 + - MAM01329c: -1 + - MAM02039c: -1 + - MAM02554c: 1 + - MAM02555c: -1 + - lower_bound: 0 - upper_bound: 1000 - - rxnFrom: "Recon3D" - - eccodes: "1.14.99.10" - - references: "PMID:9223282" + - gene_reaction_rule: "ENSG00000159228 or ENSG00000181019" + - rxnFrom: "" + - eccodes: "" + - references: "PMID:9223282;PMID:7005231;PMID:16569397" - subsystem: - "Vitamin E metabolism" - confidence_score: 0 From 35d168077472d45929cf0959f44abd489c0e3480 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 20:00:35 -0500 Subject: [PATCH 3/6] fix: replace ubiquinol with NADH and existing GPR with Complex I subunits in MAR06500 --- model/Human-GEM.yml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 92ca9829..b4d71c1f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -141151,14 +141151,17 @@ - !!omap - id: "MAR06500" - metabolites: !!omap - - MAM01328c: -1 - - MAM01329c: 1 - - MAM03102m: 1 - - MAM03103m: -1 - - lower_bound: -1000 + - MAM01328c: 1 + - MAM01329c: -1 + - MAM02039i: 4 + - MAM02039m: -5 + - MAM02552m: 1 + - MAM02553m: -1 + - lower_bound: 0 - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - references: "PMID:9223282;PMID:9223282" + - gene_reaction_rule: "ENSG00000004779 and ENSG00000023228 and ENSG00000065518 and ENSG00000090266 and ENSG00000099795 and ENSG00000109390 and ENSG00000110717 and ENSG00000115286 and ENSG00000119013 and ENSG00000119421 and ENSG00000125356 and ENSG00000128609 and ENSG00000130414 and ENSG00000131495 and ENSG00000136521 and ENSG00000139180 and ENSG00000140990 and ENSG00000145494 and ENSG00000147123 and ENSG00000147684 and ENSG00000151366 and ENSG00000158864 and ENSG00000160194 and ENSG00000164258 and ENSG00000165264 and ENSG00000166136 and ENSG00000167792 and ENSG00000168653 and ENSG00000170906 and ENSG00000174886 and ENSG00000178127 and ENSG00000183648 and ENSG00000184752 and ENSG00000184983 and ENSG00000186010 and ENSG00000189043 and ENSG00000198695 and ENSG00000198763 and ENSG00000198786 and ENSG00000198840 and ENSG00000198886 and ENSG00000198888 and ENSG00000212907 and ENSG00000213619 and ENSG00000267855" + - rxnFrom: "" + - references: "PMID:16569397" - subsystem: - "Vitamin E metabolism" - confidence_score: 0 From 6f47c7bd3425519d047487915080d6910b991f0a Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 20:09:10 -0500 Subject: [PATCH 4/6] feat: added MAR20189 to represet reduction of alpha-tocopheryl quinone by Complex III --- model/Human-GEM.yml | 17 +++++++++++++++++ model/reactions.tsv | 1 + 2 files changed, 18 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b4d71c1f..1c0d893b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -260464,6 +260464,23 @@ - subsystem: - "Transport reactions" - confidence_score: 0 + - !!omap + - id: "MAR20189" + - name: "Reduction of alpha-tocopheryl quinone by Complex III" + - metabolites: !!omap + - MAM01328c: 1 + - MAM01329c: -1 + - MAM01824m: -2 + - MAM01826m: 2 + - MAM02039i: 4 + - MAM02039m: -5 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000010256 and ENSG00000127540 and ENSG00000140740 and ENSG00000156467 and ENSG00000164405 and ENSG00000169021 and ENSG00000173660 and ENSG00000179091 and ENSG00000184076 and ENSG00000198727" + - references: "PMID:16569397" + - subsystem: + - "Miscellaneous" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" diff --git a/model/reactions.tsv b/model/reactions.tsv index 0227b7c2..4a43eb65 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12972,3 +12972,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20186" "R11929" "" "" "" "" "" "MNXR171837" "" "" "" 0 "RHEA:62609" "RHEA:62608" "" "MAR20187" "R08678" "" "" "" "" "" "MNXR112193" "" "" "" 0 "RHEA:12982" "RHEA:12981" "" "MAR20188" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20189" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From 1ba6543baede918ccfceb34852dd6d7acf48c64e Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 20:13:05 -0500 Subject: [PATCH 5/6] feat: added MAR20190 to represet reduction of alpha-tocopheryl quinone with NADH in cytosol --- model/Human-GEM.yml | 16 ++++++++++++++++ model/reactions.tsv | 1 + 2 files changed, 17 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 1c0d893b..222e9617 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -260481,6 +260481,22 @@ - subsystem: - "Miscellaneous" - confidence_score: 0 + - !!omap + - id: "MAR20190" + - name: "Reduction of alpha-tocopheryl quinone by NADH in cytosol" + - metabolites: !!omap + - MAM01328c: 1 + - MAM01329c: -1 + - MAM02039c: -1 + - MAM02552c: 1 + - MAM02553c: -1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000181019 or ENSG00000159348 or ENSG00000166394 or ENSG00000100243 or ENSG00000065615 or ENSG00000215883" + - references: "PMID:16569397;PMID:9271353" + - subsystem: + - "Miscellaneous" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" diff --git a/model/reactions.tsv b/model/reactions.tsv index 4a43eb65..1e584ba2 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12973,3 +12973,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20187" "R08678" "" "" "" "" "" "MNXR112193" "" "" "" 0 "RHEA:12982" "RHEA:12981" "" "MAR20188" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20189" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20190" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From a3340209c0663e64199e3bcbb5766af52a073c14 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 24 Dec 2024 01:32:37 +0000 Subject: [PATCH 6/6] chore: add macaw test result --- data/testResults/README.md | 2 +- data/testResults/macaw_results.csv | 8 +++++--- data/testResults/macaw_summary.md | 4 ++-- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 24c52291..56340dbc 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: -- **PR #830** (MACAW) +- **PR #945** (MACAW) - **PR #883** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index 0447ca0c..ef41f06a 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -4750,7 +4750,7 @@ MAR06471,MAM00288m + MAM01371m + MAM01597m + 2 MAM02040m + MAM02552m + MAM02630m MAR06472,MAM01227m + MAM01371m + MAM01597m + 2 MAM02040m + MAM02552m + MAM02630m --> MAM01187m + MAM01334m + 2 MAM02039m + MAM02041m + MAM02553m + MAM02759m + MAM02774m,ok,ok,ok,ok,N/A MAR06473,MAM01187m + MAM01371m + MAM01597m + 2 MAM02040m + MAM02552m + MAM02630m --> MAM01097m + MAM01261m + MAM01334m + 2 MAM02039m + MAM02041m + MAM02553m + MAM02759m,ok,ok,ok,ok,N/A MAR06476,MAM01327c + MAM02039c + MAM02555c + MAM02630c --> MAM00356c + MAM02040c + MAM02554c,ok,ok,ok,ok,N/A -MAR06500,MAM01328c + MAM03103m <=> MAM01329c + MAM03102m,ok,ok,ok,ok,N/A +MAR06500,MAM01329c + 5 MAM02039m + MAM02553m --> MAM01328c + 4 MAM02039i + MAM02552m,MAM01328c;MAM01329c,ok,ok,ok,N/A MAR06477,MAM01327r + MAM02039r + MAM02555r + MAM02630r --> MAM00356r + MAM02040r + MAM02554r,ok,ok,ok,ok,N/A MAR06478,MAM00356c + MAM02039c + 2 MAM02555c + 2 MAM02630c --> MAM00344c + 3 MAM02040c + 2 MAM02554c,ok,ok,ok,ok,N/A MAR06479,MAM00356r + MAM02039r + 2 MAM02555r + 2 MAM02630r --> MAM00344r + 3 MAM02040r + 2 MAM02554r,ok,ok,ok,ok,N/A @@ -4762,7 +4762,7 @@ MAR06490,MAM01923c + MAM03109c --> MAM01924c + MAM03106c,ok,ok,ok,ok,N/A MAR06492,MAM01924c + MAM02040c <=> MAM01923c + MAM01973c + MAM02039c,ok,ok,ok,ok,N/A MAR06495,MAM00766c + MAM03109c --> MAM01321c + MAM03106c,ok,ok,ok,ok,N/A MAR06496,MAM01321c + MAM02040c --> MAM00766c + MAM01973c + MAM02039c,ok,ok,ok,ok,N/A -MAR06501,MAM01212c <=> MAM01329c,MAM01212c,ok,ok,ok,N/A +MAR06501,MAM01212c <=> MAM01329c,MAM01212c;MAM01329c,ok,ok,ok,N/A MAR06992,MAM01374c + MAM02039c + MAM02555c + MAM02630c --> MAM01379c + MAM02040c + MAM02554c,ok,ok,ok,ok,N/A MAR06993,MAM01374c + MAM02039c + MAM02555c + MAM02630c --> MAM01378c + MAM02040c + MAM02554c,ok,ok,ok,ok,N/A MAR06994,MAM01374c + MAM02039c + MAM02555c + MAM02630c --> MAM01375c + MAM02040c + MAM02554c,ok,ok,ok,ok,N/A @@ -8750,7 +8750,7 @@ MAR03043,MAM02040e + MAM02318e <=> MAM02316e + MAM02360e,ok,ok,ok,ok,N/A MAR03044,MAM02040l + MAM02568l <=> MAM02566l + MAM02567l,MAM02566l;MAM02567l;MAM02568l,ok,ok,ok,N/A MAR03045,MAM02040e + MAM02570e <=> MAM02360e + MAM02569e,ok,ok,ok,ok,N/A MAR03046,MAM01738x + MAM02026x <=> MAM01138x,MAM01138x;MAM01738x,ok,ok,ok,N/A -MAR03047,MAM01328c + MAM03103c <=> MAM01329c + MAM03102c,ok,ok,ok,ok,N/A +MAR03047,MAM01329c + MAM02039c + MAM02555c --> MAM01328c + MAM02554c,MAM01328c;MAM01329c,ok,ok,ok,N/A MAR03048,MAM00788m + MAM01306m <=> MAM01974m + MAM02040m + MAM03151m,MAM00788m;MAM03151m,ok,ok,ok,N/A MAR03049,MAM02040c + MAM03370c <=> MAM02041c + MAM03371c,MAM03370c;MAM03371c,ok,ok,ok,N/A MAR03050,MAM02040c + MAM03372c <=> MAM02041c + MAM03373c,MAM03372c;MAM03373c,ok,ok,ok,N/A @@ -12972,3 +12972,5 @@ MAR20185,2 MAM01628m + 2 MAM01821m + MAM02555m --> 2 MAM01307m + MAM02039m + MAM MAR20186,MAM01802m + MAM02026m + MAM02039m + MAM02042m --> MAM01803m + MAM20086m,MAM02042m;MAM20086m,ok,ok,ok,N/A MAR20187,MAM02040m + MAM02630m + MAM20086m --> MAM02026m + 2 MAM02039m + MAM02949m,MAM20086m,ok,ok,ok,N/A MAR20188,MAM01098m <=> MAM01098c,MAM01098c;MAM01098m,ok,ok,ok,N/A +MAR20189,MAM01329c + 2 MAM01824m + 5 MAM02039m --> MAM01328c + 2 MAM01826m + 4 MAM02039i,MAM01328c;MAM01329c,ok,ok,ok,N/A +MAR20190,MAM01329c + MAM02039c + MAM02553c --> MAM01328c + MAM02552c,MAM01328c;MAM01329c,ok,ok,ok,N/A diff --git a/data/testResults/macaw_summary.md b/data/testResults/macaw_summary.md index 94b1288d..9eb5c041 100644 --- a/data/testResults/macaw_summary.md +++ b/data/testResults/macaw_summary.md @@ -1,6 +1,6 @@ Starting dead-end test... - - Found 1523 dead-end metabolites. - - Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends. + - Found 1525 dead-end metabolites. + - Found 1332 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends. - Found 1975 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends. Starting duplicate test... - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.