Skip to content

Remove peroxisomal genes from mitochondrial ACAD reactions #943

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Devlin-Moyer wants to merge 10 commits into
base: develop
Choose a base branch
from
Open

Remove peroxisomal genes from mitochondrial ACAD reactions #943

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
0c64152
fix: remove peroxisomal genes from mitochondrial acyl-CoA dehydrogena…
Devlin-Moyer Dec 23, 2024
61f560c
chore: add macaw test result
Devlin-Moyer Dec 23, 2024
6f98208
fix: adds ACAD11 to GPRs of MAR03107 and MAR03111 to ensure it is sti…
Devlin-Moyer Dec 23, 2024
b1e5f2b
Merge branch 'fix/acad_gprs' of https://github.com/SysBioChalmers/Hum…
Devlin-Moyer Dec 23, 2024
dca5683
chore: add gene essentiality test result
Devlin-Moyer Dec 24, 2024
9573a48
chore: merge in latest develop branch
Devlin-Moyer Feb 18, 2025
c53e836
fix: removed ACADM from GPRs of MAR03107 and MAR03111
Devlin-Moyer Feb 18, 2025
2776a5d
fix: undo addition of ACAD8 to GPRs of MAR03212 and MAR03163
Devlin-Moyer Feb 18, 2025
b47ee45
fix: add ACAD8 to GPRs of MAR03752 and MAR03784 to ensure it is still…
Devlin-Moyer Feb 20, 2025
9557ca4
fix: used wrong Ensembl ID for ACAD8 in GPRs of MAR03275 and MAR03284…
Devlin-Moyer Feb 20, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions data/testResults/gene-essential.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC
DLD1,39,2155,63,279,0.8651,0.1226,0.9716,0.1857,0.1588
GBM,35,2134,67,299,0.8556,0.1048,0.9696,0.1606,0.128
HCT116,49,2179,57,306,0.8599,0.138,0.9745,0.2126,0.1954
HELA,32,2237,74,250,0.875,0.1135,0.968,0.1649,0.1281
RPE1,15,2175,87,258,0.8639,0.05495,0.9615,0.08,0.026
all,7,2375,99,112,0.9186,0.05882,0.96,0.06222,0.01988
DLD1,50,2147,85,272,0.8602,0.1553,0.9619,0.2188,0.1739
GBM,57,2138,78,280,0.8598,0.1691,0.9648,0.2415,0.2026
HCT116,71,2179,70,289,0.8624,0.1972,0.9689,0.2834,0.2534
HELA,35,2219,106,251,0.8633,0.1224,0.9544,0.1639,0.1061
RPE1,21,2163,114,255,0.8555,0.07609,0.9499,0.1022,0.0361
all,8,2357,133,113,0.9058,0.06612,0.9466,0.06107,0.01181
22 changes: 12 additions & 10 deletions model/Human-GEM.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62692,7 +62692,7 @@
- MAM02774m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117054 or ENSG00000122971 or ENSG00000151498 or ENSG00000177646 or ENSG00000196177 or ENSG00000240303"
- gene_reaction_rule: "ENSG00000122971 or ENSG00000196177"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.99.3"
Expand Down Expand Up @@ -63045,7 +63045,7 @@
- MAM01803m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117054 or ENSG00000122971 or ENSG00000151498 or ENSG00000177646 or ENSG00000196177 or ENSG00000240303"
- gene_reaction_rule: "ENSG00000122971 or ENSG00000196177"
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.99.3"
- references: "PMID:13295225;PMID:3597357"
Expand Down Expand Up @@ -71033,7 +71033,7 @@
- MAM02468m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000122971 or ENSG00000196177"
- gene_reaction_rule: "ENSG00000151498 or ENSG00000122971 or ENSG00000196177"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.8.5"
Expand Down Expand Up @@ -71122,7 +71122,7 @@
- MAM02999m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000122971 or ENSG00000196177"
- gene_reaction_rule: "ENSG00000151498 or ENSG00000122971 or ENSG00000196177"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.8.5"
Expand Down Expand Up @@ -96075,7 +96075,7 @@
- MAM02630m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000087008 or ENSG00000161533"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646"
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.3.6"
- references: "PMID:12054595"
Expand Down Expand Up @@ -96315,7 +96315,7 @@
- MAM02630m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000087008 or ENSG00000161533"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646"
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.3.6"
- references: "PMID:11368003;PMID:9862787"
Expand Down Expand Up @@ -105177,13 +105177,14 @@
- MAM01803m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646 or ENSG00000240303"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.8.7"
- "1.3.8.8"
- "1.3.8.9"
- "1.3.99.-"
- references: "PMID:21237683"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand Down Expand Up @@ -105245,13 +105246,14 @@
- MAM01803m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646 or ENSG00000240303"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.8.7"
- "1.3.8.8"
- "1.3.8.9"
- "1.3.99.-"
- references: "PMID:21237683"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand Down Expand Up @@ -200147,7 +200149,7 @@
- MAM03333m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177"
- gene_reaction_rule: "ENSG00000115361"
- rxnFrom: "Recon3D"
- eccodes: "1.3.99.3"
- references: "PMID:1047780;PMID:11135616;PMID:8973539"
Expand Down Expand Up @@ -203271,7 +203273,7 @@
- MAM03352m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000161533"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361"
- rxnFrom: "Recon3D"
- eccodes: "1.3.3.6"
- references: "PMID:11356164;PMID:7775433"
Expand Down
Loading