remove non-metabolic isolated genes

[feiranl]

Description of the issue:

• Non-metabolic genes are discovered in the Subsystems of Isolated as below:

gene	Reasons	Subsystems	RxnIDs
ENSG00000082014	Involved in transcriptional activation and repression of select genes by chromatin remodeling	Isolated	MAR00024
ENSG00000115641	May function as a molecular transmitter linking various signaling pathways to transcriptional regulation	Isolated	MAR00024
ENSG00000120158	Does not have cyclase activity	Isolated	MAR09546
ENSG00000121486	Not methyltransferase. May play a role in motor coordination and exploratory behavior.	Isolated	MAR09519
ENSG00000124006	Core component of the 3M complex, a complex required to regulate microtubule dynamics and genome integrity.	Isolated	MAR09493
ENSG00000125686	Not lipid associated. Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes.	Isolated	MAR00024
ENSG00000127511	Not lipid associated. Acts as a transcriptional repressor.	Isolated	MAR00024
ENSG00000130589	Helicase that acts as a transcriptional coactivator.	Isolated	MAR00024
ENSG00000134317	Transcription factor involved in epithelial development	Isolated	MAR00024
ENSG00000135473	not annotated for this rxn in KEGG	Isolated	MAR09490
ENSG00000136715	Acts as a transcriptional repressor.	Isolated	MAR09464
ENSG00000148677	May play an important role in endothelial cell activation.	Isolated	MAR00024
ENSG00000162571	Inactive polyglycylase.	Isolated	MAR09505
ENSG00000167371	not sugar related, may be involved in synaptic transmission in the central nervous system.	Isolated	MAR09464
ENSG00000169375	Acts as a transcriptional repressor.	Isolated	MAR00024
ENSG00000177565	recruitment of the ubiquitin/19S proteasome complex.	Isolated	MAR00024
ENSG00000185250	Probable inactive PPIase with no peptidyl-prolyl cis-trans isomerase activity.	Isolated	MAR09492
ENSG00000185615	remove from rxn MAR00030, is not a transport gene.	Isolated;Transport reactions	MAR00030;MAR09806
ENSG00000177200	Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors.	Isolated	MAR00024

Current feature/value/output:

• The association of these genes is lack of evidence according to the provided reasons

Expected feature/value/output:

• Remove above genes from Human-GEM

I hereby confirm that I have:

• [X] Done this analysis in the main branch of the repository
• [X] Checked that a similar issue does not exist already

[haowang-bioinfo]

The gene ENSG00000185615 is currently associated with two reactions MAR00030 and MAR09806. It catalyzes the rearrangement of -S-S- bonds in the pancreas and may act as a chaperone that inhibits aggregation of misfolded proteins, this seems match well with MAR09806?

[feiranl]

Yes. It is kind of match this rxn. I was thinking even this rxn should be removed, as the protein disulfide bond formation should be protein post-translational modification process rather a metabolic rxn, but we can keep this rxn for now and the gene association.

[haowang-bioinfo]

I was thinking even this rxn should be removed, as the protein disulfide bond formation should be protein post-translational modification process rather a metabolic rxn,

yes indeed, it belongs to PTM process and was presented as a dead-end reaction in Human-GEM

[feiranl]

Since ENSG00000177565 and ENSG00000169375 are complex subunits, it ould be safe to keep them for now.