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Fix Various Issues with Lipoic Acid Biosynthesis (#830)
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* feat: added new metabolite to represent mitochondrial octanoyl-[ACP]

* feat: moved MAR06402 from c to m and removed apoA1 from reactants

* fix: turned MAM00210c into MAM00210m since the only lipoylated human proteins are strictly mitochondrial

* feat: added MAM20084m to represent a mitochondrial 4Fe4S iron-sulfur cluster

* fix: noticed that KEGG IDs for MAM00077 metabolites in metabolites.tsv were in the BiGG ID column; moved them to the KEGG ID column

* fix: moved MAR06403 from c to m and corrected various issues with the metabolites, stoichiometry, and GPR

* fix: moved MAM00208c and MAM00209c from c to m since all lipoylated human proteins are strictly mitochondrial

* fix: replaced [c] versions of remaining metabolites in MAR06404 with their [m] equivalents

* feat: added MAM20085m to represent a mitochondrial 2Fe2S iron-sulfur cluster

* feat: added MAR20184 to represent synthesis of 4Fe4S iron-sulfur clusters from 2Fe2S iron-sulfur clusters

* chore: added row to reactions.tsv for MAR20184

* feat: added MAR20185 to represent de novo synthesis of 2Fe2S in mitochondria

* feat: added MAM02042m to represent mitochondrial hydrosulfide

* feat: added MAM20086m to represent mitochondrial S-sulfanylglutathione

* feat: added MAR20186 to represent formation of GSSH from HS- and GSH by SQOR

* feat: added SQOR to GPR of MAR06911 and reordered existing genes so they're sorted by the numeric bits of their IDs

* feat: added MAR20187 to represent conversion of GSSH and O2 into GSH and sulfite by ETHE1

* feat: added MAM01098m to represent mitochondrial 5'deoxyadenosine

* feat: added MAR20188 to represent transport of 5'deoxyadenosine from mitochondria to the cytosol

* feat: added new genes to YAML file and genes.tsv for all genes in new reactions not already present

* fix: added LYRM4 to YAML file and genes.tsv because I forgot it the first time

* fix: accidentally wrote 'metfrom' instead of 'metFrom' for some of the new metabolite entries

* fix: remove duplicate function

getGenesFromGrRules is already in RAVEN

* fix: remove exportHumanGEM

use RAVEN's generic exportForGit instead

* refactor: increaseHumanGEMVersion

* chore: I/O of YAML file with latest RAVEN release

* doc: update README.md

* fix: testYamlConversion use new funcs

* chore: add macaw test result

* chore: add macaw test result

* fix: name of gene essentiality job Github Action

* chore: add macaw test result

* fix: keep test-specific PR reference in sep. lines

* chore: add macaw test result

* chore: add macaw test result

* fix: charge and empirical formula of GSSH to be consistent with GSH

* fix: added missing proton in MAR20186

* fix: genes.tsv quote all content

* fix: increaseHumanGEMVersion

* fix: testYamlConversion

* temporarily distribute YAML I/O functions

until fully merged in new RAVEN release

* fix: remove ENSG00000181562 and ENSG00000092529 from genes.tsv

* chore: add macaw test result

* fix: remove empty GPRs

* refactor: increaseHumanGEMVersion

* refactor: force specific IO functions

* chore: add gene essentiality test result

* feat: check RAVEN version increaseHumanGEMVersion

* fix: genes.tsv missing "

* fix: restore new genes in genes.tsv from earlier commit

* chore: add macaw test result

* chore: add macaw test result

---------

Co-authored-by: Eduard Kerkhoven <[email protected]>
Co-authored-by: edkerk <[email protected]>
Co-authored-by: Devlin-Moyer <[email protected]>
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@Devlin-Moyer @edkerk
4 people authored Dec 23, 2024
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4 changes: 2 additions & 2 deletions data/testResults/README.md
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Expand Up @@ -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 #942** (MACAW)
- **PR #830** (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.
Expand All @@ -25,4 +25,4 @@ It is possible for a single reaction to fit in multiple of the above categories.
### 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.
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.
23 changes: 14 additions & 9 deletions data/testResults/macaw_results.csv
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Expand Up @@ -682,8 +682,8 @@ MAR05393,6 MAM02040c + MAM02981c --> 6 MAM01974c + MAM02980c,ok,ok,ok,ok,N/A
MAR06409,MAM02039m + MAM02393m + MAM02553m <=> MAM01701m + MAM02552m,only when going forwards,ok,ok,ok,N/A
MAR07702,MAM02007c + MAM02039c + MAM02555c <=> MAM01998c + MAM02554c,ok,ok,ok,ok,N/A
MAR07703,MAM01998c + MAM02630c --> MAM02007c + MAM02041c,ok,ok,ok,ok,N/A
MAR08433,MAM00209c + MAM01986m + MAM02039m --> MAM01596m + MAM02878m,ok,ok,ok,ok,N/A
MAR08434,MAM02878m + MAM02980m --> MAM00208c + MAM01045m + MAM02039m + MAM02578m,ok,ok,ok,ok,N/A
MAR08433,MAM00209m + MAM01986m + MAM02039m --> MAM01596m + MAM02878m,ok,ok,ok,ok,N/A
MAR08434,MAM02878m + MAM02980m --> MAM00208m + MAM01045m + MAM02039m + MAM02578m,ok,ok,ok,ok,N/A
MAR08439,MAM01708m + MAM01802m + MAM02040m --> MAM01803m + MAM01831m + MAM02880m,ok,ok,ok,ok,N/A
MAR08440,MAM01394m + MAM02040m + MAM02552m --> MAM01393m + 2 MAM02039m + MAM02553m,ok,ok,ok,ok,N/A
MAR08441,MAM01513m + MAM01802m --> MAM01394m + MAM01803m,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -1659,9 +1659,9 @@ MAR02468,MAM00314r + MAM03109r --> MAM00323r + MAM02039r + MAM03106r,ok,ok,ok,ok
MAR02469,MAM00314c + MAM03109c <=> MAM00327c + MAM02039c + MAM03106c,only when going backwards,ok,ok,ok,N/A
MAR02470,MAM00314r + MAM03109r --> MAM00327r + MAM02039r + MAM03106r,ok,ok,ok,ok,N/A
MAR06397,MAM02039c + MAM02394c + MAM02553c <=> MAM01702c + MAM02552c,ok,ok,ok,ok,N/A
MAR06402,MAM01350c + MAM02643c --> MAM00184c + MAM00210c,ok,ok,ok,ok,N/A
MAR06403,MAM00210c + 5 MAM02039c + 7 MAM02555c + 2 MAM02682c + 2 MAM02877c --> MAM00209c + 2 MAM01098c + 6 MAM02040c + 2 MAM02471c + 7 MAM02554c + 2 MAM02681c,ok,ok,ok,ok,N/A
MAR06404,MAM00209c + MAM02039c + MAM02553c <=> MAM00208c + MAM02552c,only when going forwards,ok,ok,ok,N/A
MAR06402,MAM02643m --> MAM00210m + MAM02484m,MAM02484m;MAM00210m;MAM02643m,ok,ok,ok,N/A
MAR06403,MAM00210m + 3 MAM02039m + MAM02555m + 2 MAM02877m + MAM20084m --> MAM00208m + 2 MAM01098m + 4 MAM01821m + 2 MAM02042m + 2 MAM02471m + MAM02554m,MAM00210m;MAM01098m;MAM02042m;MAM20084m,ok,ok,ok,N/A
MAR06404,MAM00209m + MAM02039m + MAM02553m <=> MAM00208m + MAM02552m,only when going forwards,ok,ok,ok,N/A
MAR02472,MAM02039c + MAM02390c + MAM02555c + MAM02630c --> MAM00108c + 2 MAM02040c + MAM02554c,ok,ok,ok,ok,N/A
MAR02475,MAM00108c + MAM02039c + MAM02444c --> MAM00811c + MAM01596c + MAM01597c,ok,ok,ok,ok,N/A
MAR02478,MAM00811c + MAM02039c + MAM02555c --> MAM00708c + MAM02554c,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -6593,7 +6593,7 @@ MAR09623,MAM01306c + MAM01659e --> MAM01306e + MAM01659c,ok,ok,ok,ok,N/A
MAR09624,MAM01306c + MAM01789e --> MAM01306e + MAM01789c,ok,ok,ok,ok,N/A
MAR09635,MAM02022c <=> MAM02022e,MAM02022c;MAM02022e,ok,ok,ok,N/A
MAR09636,MAM02384c --> MAM02384e,ok,ok,ok,ok,N/A
MAR09637,MAM01098c <=> MAM01098e,only when going backwards,ok,ok,ok,N/A
MAR09637,MAM01098c <=> MAM01098e,MAM01098c;MAM01098e,ok,ok,ok,N/A
MAR09638,MAM00969c <=> MAM00969e,ok,ok,ok,ok,N/A
MAR09639,MAM01315c <=> MAM01315e,ok,ok,ok,ok,N/A
MAR09640,MAM02328c <=> MAM02328e,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -7814,7 +7814,7 @@ MAR09294,MAM01614e <=> ,ok,ok,ok,ok,N/A
MAR09295,MAM01630e <=> ,ok,ok,ok,ok,N/A
MAR09296,MAM01668e <=> ,ok,ok,ok,ok,N/A
MAR09297,MAM01666e <=> ,ok,ok,ok,ok,N/A
MAR09298,MAM01098e <=> ,only when going backwards,ok,ok,ok,N/A
MAR09298,MAM01098e <=> ,MAM01098e,ok,ok,ok,N/A
MAR09299,MAM01647e <=> ,MAM01647e,ok,ok,ok,N/A
MAR09300,MAM01669e <=> ,ok,ok,ok,ok,N/A
MAR09301,MAM01655e <=> ,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -8018,7 +8018,7 @@ MAR09730,MAM01308e <=> ,ok,ok,ok,ok,N/A
MAR09725,MAM02554c + MAM02555n <=> MAM02554n + MAM02555c,only when going forwards,ok,ok,ok,N/A
MAR00031,0.19 MAM00240c + 0.0014 MAM00511c + 0.0024 MAM00560c + 0.0006 MAM00656c + 0.005 MAM01450c + 0.34 MAM01451c + 0.0008 MAM02629c + 0.0092 MAM02684c + 0.0034 MAM02685c + 0.0016 MAM02750c + 0.0002 MAM02808c + 0.0004 MAM02908c + 0.44 MAM02958c + 0.005 MAM10005c --> MAM02392c,ok,ok,ok,ok,N/A
MAR00021,MAM01307c + MAM01365c + MAM01369c + MAM01370c + MAM01450c + MAM01451r + MAM01589c + MAM01602c + MAM01628c + MAM01721n + MAM01722n + MAM01974c + MAM01975c + MAM01986c + MAM02125c + MAM02184c + MAM02360c + MAM02392c + MAM02426c + MAM02471c + MAM02724c + MAM02733c + MAM02750c + MAM02770c + MAM02847c + MAM02896c + MAM02908c + MAM02993c + MAM03089c + MAM03101c + MAM03135c + MAM03161c --> MAM03970c,ok,ok,ok,ok,N/A
MAR00022,MAM00209c + MAM01401c + MAM01597c + MAM01600m + MAM01631m + MAM01803c + MAM02348c + MAM02553c + MAM02555c + MAM02842c + MAM02978c + MAM02980c + MAM03102m + 0.1 MAM03139c + 0.1 MAM03140c + 0.1 MAM03143c --> MAM01602c,ok,ok,ok,ok,N/A
MAR00022,MAM00209m + MAM01401c + MAM01597c + MAM01600m + MAM01631m + MAM01803c + MAM02348c + MAM02553c + MAM02555c + MAM02842c + MAM02978c + MAM02980c + MAM03102m + 0.1 MAM03139c + 0.1 MAM03140c + 0.1 MAM03143c --> MAM01602c,ok,ok,ok,ok,N/A
MAR00023,MAM00291c + MAM00427c + MAM00427r + MAM01008c + MAM01008r + MAM01022c + MAM01022r + MAM01024c + MAM01024r + MAM01026r + MAM01028c + MAM01028r + MAM01030c + MAM01030r + MAM01031c + MAM01031r + MAM01032c + MAM01060c + MAM01232c + MAM02624c --> MAM03139c,ok,ok,ok,ok,N/A
MAR00033,MAM00611c + MAM00611m + MAM00622c + MAM00622m --> MAM03140c,ok,ok,ok,ok,N/A
MAR00034,MAM00766c + MAM01924c --> MAM03143c,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -12951,7 +12951,7 @@ MAR20164,MAM01623c <=> MAM01623m,ok,ok,ok,ok,N/A
MAR20165,MAM02034c <=> MAM02034m,ok,ok,ok,ok,N/A
MAR20166,MAM03130c <=> MAM03130m,ok,ok,ok,ok,N/A
MAR20167,MAM03103m + MAM20019c <=> MAM01828c + MAM03102m,ok,ok,ok,ok,N/A
MAR20168,MAM00209c --> MAM02393m,ok,ok,ok,ok,N/A
MAR20168,MAM00209m --> MAM02393m,ok,ok,ok,ok,N/A
MAR20169,MAM01412c + MAM02040c --> MAM01410c + MAM01597c + MAM02039c,ok,ok,ok,ok,N/A
MAR20170,MAM02040c + MAM02644c --> MAM01597c + MAM02039c + MAM02642c,ok,ok,ok,ok,N/A
MAR20171,MAM01650c + MAM02040c --> MAM01597c + MAM01648c + MAM02039c,ok,ok,ok,ok,N/A
Expand All @@ -12967,3 +12967,8 @@ MAR20180,MAM00077e <=> ,MAM00077e,ok,ok,ok,N/A
MAR20181,MAM02983c + MAM02984m <=> MAM02983m + MAM02984c,ok,ok,ok,ok,N/A
MAR20182,MAM01642c + MAM02983m <=> MAM01642m + MAM02983c,ok,ok,ok,ok,N/A
MAR20183,MAM01642c + MAM02984m <=> MAM01642m + MAM02984c,ok,ok,ok,ok,N/A
MAR20184,2 MAM01371m + 2 MAM02040m + MAM02555m + 2 MAM20085m --> 2 MAM01285m + 3 MAM02039m + MAM02554m + 2 MAM02751m + MAM20084m,MAM20084m;MAM20085m,ok,ok,ok,N/A
MAR20185,2 MAM01628m + 2 MAM01821m + MAM02555m --> 2 MAM01307m + MAM02039m + MAM02554m + MAM20085m,MAM20085m,ok,ok,ok,N/A
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
6 changes: 3 additions & 3 deletions data/testResults/macaw_summary.md
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@@ -1,7 +1,7 @@
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.
- Found 1523 dead-end metabolites.
- Found 1328 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.
- Found 447 reactions that were some type of duplicate:
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