QC for skipping molecular events during load of Reactome metabolic models #366
Description
This QC is to check that molecular events are skipped and replaced with causal relations in the Reactome metabolic pathways load. The following models should be examined. Checking off a model means it passed the test. Otherwise, notes will be added below.
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-1660661? CERT1-2 binds ceramide (R-HSA-429699), CERT1-2 releases its bound ceramide... (R-HSA-429683) and CERT1-2 dissociates from the ER membrane (R-HSA-429694) should all be removed from the model due to edits.
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-196836? DeHA hydrolyses to 2,3-DKG (R-HSA-9640307) spontaneous, Asc.- radical dissociates to AscH- and DeHA (R-HSA-9640302) spontaneous, 2,3-DKG hydrolyses to ERU and oxalate (R-HSA-9640321) spontaneous
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-189451? HMBL spontaneously transforms to URO1 (R-HSA-190168) spontaneous,ALB binds extracellular heme (R-HSA-9661419) should be retained and have been edited
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-9759218? Cob(I)alamin bound to MMACHC is oxidized to cob(II)alamin (R-HSA-9759549) should be oxidoreductase activity with no catalyst.
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-71288? phosphocreatine + H2O => creatinine + orthophosphate (R-HSA-71287) should be removed and is last step
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-75105? Formation of fatty acid synthase (FAS) dimer (R-HSA-163756) should be merged into Conversion of malonyl-CoA and acetyl-CoA to palmitate (R-HSA-75872) same MF and same enabler
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-9018682? Non-enzymatic hydrolysis hydrolyses 13(S),14(S)-epoxy-DHA to 7-epi-MaR1 (R-HSA-9026544) spontaneous
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-163560? This one is a good one 2 phosphorylated HSL monomers -> phosphorylated HSL dimer (R-HSA-163602) dimerization, Phosphorylated HSL dimer translocates from the cytosol to the lipid particle (R-HSA-163554), inferred transporter activity Both should collapse
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-975634? Parenchymal atROL translocates to HSCs (R-HSA-2404144), Nascent CMs transform into mature CMs (R-HSA-2395784)
- http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-1474151? Ferrous iron reduces the BH3 radical back to BH4 (R-HSA-1497883), BH2 binding can lead to eNOS uncoupling (R-HSA-1497796), The BH3 radical can decay to dihydrobiopterin (BH2) (R-HSA-1497863), BH4 is oxidised to the BH3 radical during the eNOS catalytic cycle (R-HSA-1497824), Peroxynitrite can oxidise BH4 to the BH3 radical (R-HSA-1497866), Ascorbate can reduce the BH3 radical back to BH4 (R-HSA-1497855)