diff --git a/.github/workflows/commentsFromTests.md b/.github/workflows/commentGeneEssential.md
similarity index 61%
rename from .github/workflows/commentsFromTests.md
rename to .github/workflows/commentGeneEssential.md
index 4c5857ea..dd2ba900 100644
--- a/.github/workflows/commentsFromTests.md
+++ b/.github/workflows/commentGeneEssential.md
@@ -1,9 +1,7 @@
-This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the macaw test:
+This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the gene essentiality test:
{TEST_RESULTS}
-A more detailed output from this test run is also committed to `data/macawResults/macaw_results.csv`.
-
> _Note: In the case of multiple test runs, this post will be edited._
diff --git a/.github/workflows/commentMacaw.md b/.github/workflows/commentMacaw.md
new file mode 100644
index 00000000..022ee3d0
--- /dev/null
+++ b/.github/workflows/commentMacaw.md
@@ -0,0 +1,9 @@
+This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the [MACAW](https://github.com/Devlin-Moyer/macaw) test:
+
+
+{TEST_RESULTS}
+
+
+This and a more detailed output from MACAW are also committed to `data/macawResults/`.
+
+> _Note: In the case of multiple test runs, this post will be edited._
diff --git a/.github/workflows/gene-essentiality.yml b/.github/workflows/gene-essentiality.yml
new file mode 100644
index 00000000..b92c87d6
--- /dev/null
+++ b/.github/workflows/gene-essentiality.yml
@@ -0,0 +1,80 @@
+name: Check gene essentiality with Hart 2015
+
+on:
+ pull_request:
+ branches:
+ - "main"
+ - "develop"
+
+jobs:
+ check-metabolictasks:
+ runs-on: self-hosted
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v4
+
+ - name: Fetch RAVEN
+ uses: actions/checkout@v4
+ with:
+ repository: "SysBioChalmers/RAVEN"
+ path: "RAVEN"
+
+ - name: Run gene essentiality
+ id: essentiality
+ run: >
+ TEST_RESULTS=$(/usr/local/bin/matlab -batch
+ "warning('off', 'MATLAB:rmpath:DirNotFound');
+ rmpath(genpath('/home/m/ecModels-dependencies/RAVEN'));
+ rmpath(genpath('/home/m/actions-runner'));
+ addpath(genpath('.'));
+ setRavenSolver('gurobi');
+ ihuman = readYAMLmodel('model/Human-GEM.yml');
+ taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt');
+ [~, eGenes] = evalc('estimateEssentialGenes(ihuman, ''Hart2015_RNAseq.txt'', taskStruct);');
+ output = transpose(evaluateHart2015Essentiality(eGenes));
+ fid = fopen('data/testResults/gene-essential.csv','w');
+ fprintf(fid,[repmat('%s,',1,9) '%s\n'],output{:,1});
+ fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,5) '\n'],output{:,2:end});
+ fclose(fid);
+ disp(cell2table(transpose(output(:,2:end)),'VariableNames',output(:,1)));") &&
+ echo "$TEST_RESULTS" &&
+ PARSED_RESULTS="${TEST_RESULTS//$'\n'/'
'}" &&
+ PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'
'}" &&
+ echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT
+
+ - name: Mention PR# in README.md
+ env:
+ PR_NUMBER: ${{ github.event.number }}
+ run: sed -i -e "s/[[:digit:]]\{3,4\}\*\* (gene /$PR_NUMBER\*\* (gene /" data/testResults/README.md
+
+ - name: Update local branch before committing changes
+ env:
+ BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+ run: |
+ git stash
+ git fetch
+ git checkout $BRANCH_NAME
+ if git stash list | grep -q 'stash@{'; then
+ git stash pop
+ fi
+
+ - name: Auto-commit results
+ uses: stefanzweifel/git-auto-commit-action@v5
+ with:
+ commit_user_name: memote-bot
+ commit_message: "chore: add gene essentiality test result"
+ file_pattern: data/testResults/*
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ PR_NUMBER: ${{ github.event.number }}
+
+ - name: Post comment
+ uses: NejcZdovc/comment-pr@v2
+ with:
+ file: "commentGeneEssential.md"
+ identifier: "GITHUB_COMMENT_GENE"
+ env:
+ GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+ TEST_RESULTS: ${{steps.essentiality.outputs.results}}
+ GH_ACTION_RUN: ${{github.run_id}}
diff --git a/.github/workflows/macaw-tests.yml b/.github/workflows/macaw-tests.yml
index 90af0ee7..be78f38d 100644
--- a/.github/workflows/macaw-tests.yml
+++ b/.github/workflows/macaw-tests.yml
@@ -31,18 +31,30 @@ jobs:
PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'
'}"
echo $PARSED_RESULTS
echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT
+ printf "$TEST_RESULTS" > data/testResults/macaw_summary.md
- name: Mention PR# in README.md
env:
PR_NUMBER: ${{ github.event.number }}
- run: sed -i -e "s/#[[:digit:]]\{3,4\}/#$PR_NUMBER/g" data/macawResults/README.md
-
+ run: sed -i -e "s/[[:digit:]]\{3,4\}\*\* (MACAW)/$PR_NUMBER\*\* (MACAW)/" data/testResults/README.md
+
+ - name: Update local branch before committing changes
+ env:
+ BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+ run: |
+ git stash
+ git fetch
+ git checkout $BRANCH_NAME
+ if git stash list | grep -q 'stash@{'; then
+ git stash pop
+ fi
+
- name: Auto-commit results
uses: stefanzweifel/git-auto-commit-action@v4
with:
commit_user_name: memote-bot
commit_message: "chore: add macaw test result"
- file_pattern: data/macawResults/*
+ file_pattern: data/testResults/*
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
PR_NUMBER: ${{ github.event.number }}
@@ -50,7 +62,8 @@ jobs:
- name: Post comment
uses: NejcZdovc/comment-pr@v2
with:
- file: "commentsFromTests.md"
+ file: "commentMacaw.md"
+ identifier: "GITHUB_COMMENT_MACAW"
env:
GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
TEST_RESULTS: ${{steps.macaw-run.outputs.results}}
diff --git a/code/estimateEssentialGenes.m b/code/test/estimateEssentialGenes.m
similarity index 100%
rename from code/estimateEssentialGenes.m
rename to code/test/estimateEssentialGenes.m
diff --git a/code/evalGeneEssentialityPred.m b/code/test/evalGeneEssentialityPred.m
similarity index 100%
rename from code/evalGeneEssentialityPred.m
rename to code/test/evalGeneEssentialityPred.m
diff --git a/code/evaluateHart2015Essentiality.m b/code/test/evaluateHart2015Essentiality.m
similarity index 88%
rename from code/evaluateHart2015Essentiality.m
rename to code/test/evaluateHart2015Essentiality.m
index 1ae32aa8..8fd1cb02 100644
--- a/code/evaluateHart2015Essentiality.m
+++ b/code/test/evaluateHart2015Essentiality.m
@@ -31,16 +31,16 @@
% Table S2 from the Hart2015 datasets:
% In this study, essential genes are, by definition, a subset of fitness genes
x = readtable('Hart2015_TableS2.xlsx');
-
+
% remove duplicated rows (MARCH1 and MARCH2 genes)
ind1 = find(ismember(x.Gene,'MARCH1'),1,'last');
ind2 = find(ismember(x.Gene,'MARCH2'),1,'last');
x([ind1;ind2],:) = [];
-
+
% extract gene list and cell types
genes = x.Gene;
celltypes = regexprep(upper(x.Properties.VariableNames(3:7)'),'BF_','');
-
+
% for each cell type, determine the "fitness" genes, defined as those with
% a 5% FDRs were chosen as thresholds (the values are extracted from the
% supporting information of the Hart 2015 paper. Genes observed in 3 or more
@@ -63,7 +63,7 @@
% also get the genes that were essential in all 5 cell lines ("all")
celltypes(end+1) = {'all'};
fitness_mat(:,end+1) = all(fitness_mat == 1,2);
-
+
% put Hart2015 essentiality data into data structure for comparison
expdata = {};
expdata.genes = genes;
@@ -94,12 +94,12 @@
% calculate true and false positives and negatives
[TP,TN,FP,FN,Penr] = deal(nan(numel(tissues),1)); % initialize variables
for i = 1:numel(tissues)
-
+
[~,tissue_ind] = ismember(tissues(i), expdata.tissues);
if tissue_ind == 0
continue % a few tissues are missing from the DepMap dataset
end
-
+
modelGenes = eGenes.refModel.genes;
if strcmpi(tissues{i},'all')
modelEssential = modelGenes(sum(modelPred,2) == size(modelPred,2));
@@ -107,17 +107,18 @@
modelEssential = modelGenes(modelPred(:,i));
end
modelNonEssential = setdiff(modelGenes,modelEssential);
-
+
expGenes = expdata.genes(~isnan(expdata.essential(:,tissue_ind)));
expEssential = expdata.genes(expdata.essential(:,tissue_ind) == 1);
expNonEssential = setdiff(expGenes,expEssential);
-
+
TP(i) = sum(ismember(modelEssential, expEssential)); % true positives
TN(i) = sum(ismember(modelNonEssential, expNonEssential)); % true negatives
FP(i) = sum(ismember(modelEssential, expNonEssential)); % false positives
- FN(i) = sum(ismember(modelNonEssential, expEssential)); % false negatives
+ FN(i) = sum(ismember(modelNonEssential, expEssential)); % false negatives
- Penr(i) = EnrichmentTest(intersect(modelGenes,expGenes), intersect(modelEssential,expGenes), intersect(expEssential,modelGenes));
+ % Requires Statistics and Machine Learning Toolbox
+ %Penr(i) = EnrichmentTest(intersect(modelGenes,expGenes), intersect(modelEssential,expGenes), intersect(expEssential,modelGenes));
end
% calculate some metrics
@@ -126,13 +127,15 @@
accuracy = (TP + TN)./(TP + TN + FP + FN);
F1 = 2*TP./(2*TP + FP + FN);
MCC = ((TP.*TN) - (FP.*FN))./sqrt((TP+FP).*(TP+FN).*(TN+FP).*(TN+FN)); % Matthews correlation coefficient
-PenrAdj = adjust_pvalues(Penr,'Benjamini');
+%PenrAdj = adjust_pvalues(Penr,'Benjamini');
% get results for cell types
-results = [{'cellLine','TP','TN','FP','FN','accuracy','sensitivity','specificity','F1','MCC','Penr','logPenr','PenrAdj','logPenrAdj'};
- [tissues, num2cell([TP, TN, FP, FN, accuracy, sensitivity, specificity, F1, MCC, Penr, -log10(Penr), PenrAdj, -log10(PenrAdj)])]];
-
+results = [{'cellLine','TP','TN','FP','FN','accuracy','sensitivity','specificity','F1','MCC'};
+ [tissues, num2cell([TP, TN, FP, FN, accuracy, sensitivity, specificity, F1, MCC])]];
+% Including Penr results
+%results = [{'cellLine','TP','TN','FP','FN','accuracy','sensitivity','specificity','F1','MCC','Penr','logPenr','PenrAdj','logPenrAdj'};
+% [tissues, num2cell([TP, TN, FP, FN, accuracy, sensitivity, specificity, F1, MCC, Penr, -log10(Penr), PenrAdj, -log10(PenrAdj)])]];
end
function [penr,pdep] = EnrichmentTest(pop,sample,successes)
diff --git a/code/test/macawTests.py b/code/test/macawTests.py
index 92f71544..7b285639 100644
--- a/code/test/macawTests.py
+++ b/code/test/macawTests.py
@@ -5,4 +5,4 @@
(dead_end_results, dead_end_edges) = dead_end_test(model)
(duplicate_results, duplicate_edges) = duplicate_test(model)
output = dead_end_results.merge(duplicate_results)
-output.to_csv('data/macawResults/macaw_results.csv', index = False)
\ No newline at end of file
+output.to_csv('data/testResults/macaw_results.csv', index = False)
\ No newline at end of file
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/macawResults/README.md b/data/testResults/README.md
similarity index 65%
rename from data/macawResults/README.md
rename to data/testResults/README.md
index f3aa5afe..78746c32 100644
--- a/data/macawResults/README.md
+++ b/data/testResults/README.md
@@ -1,13 +1,13 @@
-# MACAW results
+# Test results
-The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests.
+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 #885**, 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 #928** (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.
-### `dead_end_test`
+### 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.
-### `duplicate_test`
+### MACAW: `duplicate_test`
Identifies sets of reactions that may be duplicates of each other because they:
- Involve exactly the same metabolites with exactly the same stoichiometric coefficients (but potentially different associated genes).
@@ -15,4 +15,9 @@ Identifies sets of reactions that may be duplicates of each other because they:
- Involve exactly the same metabolites, but with different stoichiometric coefficients.
- Represent the oxidation and/or reduction of the same metabolite, but use different electron acceptors/donors from the given list of pairs of oxidized and reduced forms of various electron carriers (e.g. NAD(H), NADP(H), FAD(H2), ubiquinone/ubiquinol, cytochromes).
-It is possible for a single reaction to fit in multiple of the above categories. There are sometimes cases where sets of reactions that fall into one of the above categories are completely legitimate representations of real biochemistry (e.g. separate irreversible reactions for importing vs exporting the same metabolite because two different transporters encoded by different genes are each responsible for transporting that metabolite in only one direction, enzymes that can use NAD(H) or NADP(H) interchangeably to catalyze the same redox reaction), but reactions that meet these criteria are generally worth close examination to ensure that they should actually all exist as separate reactions.
\ No newline at end of file
+It is possible for a single reaction to fit in multiple of the above categories. There are sometimes cases where sets of reactions that fall into one of the above categories are completely legitimate representations of real biochemistry (e.g. separate irreversible reactions for importing vs exporting the same metabolite because two different transporters encoded by different genes are each responsible for transporting that metabolite in only one direction, enzymes that can use NAD(H) or NADP(H) interchangeably to catalyze the same redox reaction), but reactions that meet these criteria are generally worth close examination to ensure that they should actually all exist as separate reactions.
+
+### Cell-line specific gene essentiality
+Evaluate gene essentiality predictions in 5 cell-line specific GEMs with experimental fitness data gathered from the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015).
+
+Cell-line specific GEMs are constructed with tINIT2 for DLD1, GBM, HCT116, HeLa and RPE1 cell lines. Then, the `metabolicTasks_Essential.txt` list of tasks is used to identify essential genes in each of these models. The predicted gene essentiality is compared to results from a high-throughput CRISPR-Cas9 screen for identifying genes that affect fitness. Only the summary statistics of this comparison are kept.
\ No newline at end of file
diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv
new file mode 100644
index 00000000..7a3cef63
--- /dev/null
+++ b/data/testResults/gene-essential.csv
@@ -0,0 +1,7 @@
+cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC
+DLD1,36,2185,59,279,0.8679,0.1143,0.9737,0.1756,0.1529
+GBM,34,2165,61,298,0.8597,0.1024,0.9726,0.1593,0.1333
+HCT116,46,2207,53,309,0.8616,0.1296,0.9765,0.2026,0.1905
+HELA,30,2263,69,254,0.8765,0.1056,0.9704,0.1567,0.124
+RPE1,14,2204,81,259,0.8671,0.05128,0.9646,0.07609,0.02585
+all,7,2408,92,109,0.9232,0.06034,0.9632,0.06512,0.0254
diff --git a/data/macawResults/macaw_results.csv b/data/testResults/macaw_results.csv
similarity index 99%
rename from data/macawResults/macaw_results.csv
rename to data/testResults/macaw_results.csv
index aa73eeed..112e0ccf 100644
--- a/data/macawResults/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/data/testResults/macaw_summary.md b/data/testResults/macaw_summary.md
new file mode 100644
index 00000000..26f5f7ab
--- /dev/null
+++ b/data/testResults/macaw_summary.md
@@ -0,0 +1,10 @@
+Starting dead-end test...
+ - Found 1514 dead-end metabolites.
+ - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
+ - Found 1977 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.
+ - Found 447 reactions that were some type of duplicate:
+ - 0 were completely identical to at least one other reaction.
+ - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
+ - 447 involve the same metabolites but with different coefficients as at least one other reaction.
\ No newline at end of file
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 11251b56..872fb3e6 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"
@@ -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"
@@ -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"
@@ -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
@@ -131779,7 +131779,7 @@
- MAM02555c: -1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
+ - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72"
@@ -131818,7 +131818,7 @@
- MAM02555m: 1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
+ - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72"
@@ -134237,7 +134237,7 @@
- MAM02877c: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000135929"
+ - gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.1.1.103"
@@ -134255,7 +134255,7 @@
- MAM02877c: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000135929"
+ - gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.1.1.103"
@@ -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.-"
@@ -159340,7 +159340,7 @@
- MAM02630c: -1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.14.14.1"
@@ -159382,7 +159382,7 @@
- MAM02630c: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.14.14.1"
@@ -159695,7 +159695,7 @@
- MAM03043c: 1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
+ - gene_reaction_rule: "ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.1"
@@ -159971,7 +159971,7 @@
- MAM02630c: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.14.14.1"
@@ -160084,7 +160084,7 @@
- MAM02555c: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000104808 or ENSG00000117594 or ENSG00000151632 or ENSG00000159228 or ENSG00000159231 or ENSG00000187134 or ENSG00000196139 or ENSG00000198610"
+ - gene_reaction_rule: "ENSG00000104808 or ENSG00000151632 or ENSG00000159228 or ENSG00000159231 or ENSG00000187134 or ENSG00000196139 or ENSG00000198610"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.146;1.1.1.184;1.3.1.20"
@@ -160786,7 +160786,7 @@
- MAM02630c: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000108242 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000106258 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.14.14.1"
@@ -161269,7 +161269,7 @@
- MAM02156c: -1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
+ - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000167419"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.11.1.7"
@@ -161288,7 +161288,7 @@
- MAM02591c: 1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
+ - gene_reaction_rule: "ENSG00000121053 or ENSG00000130508 or ENSG00000167419"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.11.1.7"
@@ -161306,7 +161306,7 @@
- MAM02754e: 1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000006534 or ENSG00000014257 or ENSG00000102575 or ENSG00000134575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162551 or ENSG00000162836 or ENSG00000163283 or ENSG00000163286 or ENSG00000163295 or ENSG00000184254"
+ - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000134575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162551 or ENSG00000162836 or ENSG00000163283 or ENSG00000163286 or ENSG00000163295"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.1;3.1.3.2;3.1.3.41"
@@ -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"
@@ -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"
@@ -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"
@@ -223519,7 +223471,7 @@
- MAM03727c: 1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+ - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "2.3.1.21"
@@ -231853,7 +231805,7 @@
- MAM03333m: -1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000161533 or ENSG00000196177"
+ - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.3.99.3"
@@ -232327,7 +232279,7 @@
- MAM02766x: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000068366 or ENSG00000103740 or ENSG00000119673 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000177465 or ENSG00000197142"
+ - gene_reaction_rule: "ENSG00000140284"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "6.2.1.3"
@@ -235503,7 +235455,7 @@
- MAM03381r: 1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.14.14.1"
@@ -235704,7 +235656,7 @@
- MAM03386r: 1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.14.14.1"
@@ -235797,7 +235749,7 @@
- MAM03388r: 1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
+ - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.14.14.1"
@@ -237386,7 +237338,7 @@
- MAM03488c: 1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+ - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
@@ -237965,7 +237917,7 @@
- MAM03496c: 1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+ - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
@@ -241109,7 +241061,7 @@
- MAM03243c: 1
- lower_bound: -1000
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
+ - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560"
- rxnNotes: "http://www.perkinelmergenetics.com/3Hydroxy3MethylglutarylCoALyaseDeficiency.html"
- rxnFrom: "Recon3D"
- eccodes: ""
@@ -241211,7 +241163,7 @@
- MAM03409x: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "ENSG00000060971 and ENSG00000113790 and ENSG00000133835 and ENSG00000161533"
+ - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835) and (ENSG00000060971 or ENSG00000116171)"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
@@ -272576,7 +272528,7 @@
- MAM03922x: -1
- lower_bound: 0
- upper_bound: 1000
- - gene_reaction_rule: "(ENSG00000113790 and ENSG00000161533) or (ENSG00000104823 and ENSG00000161533)"
+ - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835)"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.3.3.6;4.2.1.17"
@@ -305846,9 +305798,6 @@
- !!omap
- id: "ENSG00000092295"
- name: "TGM1"
- - !!omap
- - id: "ENSG00000092529"
- - name: "CAPN3"
- !!omap
- id: "ENSG00000092621"
- name: "PHGDH"
@@ -311945,9 +311894,6 @@
- !!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 60dfa7db..a34f0f10 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"
@@ -2406,7 +2405,6 @@ 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
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"