Genes expressed in peroxisome but found in GPR of beta-oxidation reactions in mitochondria

[haowang-bioinfo]

Current behavior:

Inspired by #746, the following peroxisome genes are found by this code through following steps:

1. find reactions that are in mitochondria compartment from Fatty acid oxidation subsystem
2. go through these reactions and check each gene's compartment based on the annotation in genes.tsv
3. report the ones that suppose to be expressed only in peroxisome compartment

Reaction	Peroxisome gene	Equation	GPR	GPR in gene name
MAR02028	ENSG00000115425	NADP+ + palmitoyl-CoA <=> (2E)-hexadecenoyl-CoA + H+ + NADPH	ENSG00000115425 or ENSG00000116353	PECR or MECR
MAR02148	ENSG00000115425	NADP+ + octanoyl-CoA <=> (2E)-octenoyl-CoA + H+ + NADPH	ENSG00000115425 or ENSG00000116353	PECR or MECR
MAR02149	ENSG00000115425	lauroyl-CoA + NADP+ <=> (2E)-dodecenoyl-CoA + H+ + NADPH	ENSG00000115425 or ENSG00000116353	PECR or MECR
MAR02183	ENSG00000115425	myristoyl-CoA + NADP+ <=> (2E)-tetradecenoyl-CoA + H+ + NADPH	ENSG00000115425 or ENSG00000116353	PECR or MECR
MAR02187	ENSG00000115425	decanoyl-CoA + NADP+ <=> (2E)-decenoyl-CoA + H+ + NADPH	ENSG00000115425 or ENSG00000116353	PECR or MECR
MAR02207	ENSG00000115425	(2E)-hexenoyl-CoA + H+ + NADPH <=> hexanoyl-CoA + NADP+	ENSG00000115425 or ENSG00000116353	PECR or MECR
MAR02381	ENSG00000060971	3-oxooleoyl-CoA + CoA --> acetyl-CoA + palmitoleoyl-CoA	(ENSG00000138029 and ENSG00000167315) or (ENSG00000060971 and ENSG00000138029)	(HADHB and ACAA2) or (ACAA1 and HADHB)
MAR03269	ENSG00000133835	NAD+ + 3(S)-3-Hydroxydodecen-(5Z)-Oyl Coenzyme A <=> H+ + NADH + 3-Oxolaur-Cis-5-Enoyl Coenzyme A	ENSG00000072506 or ENSG00000084754 or ENSG00000113790 or ENSG00000133835 or ENSG00000138029 or ENSG00000138796	HSD17B10 or HADHA or EHHADH or HSD17B4 or HADHB or HADH
MAR03269	ENSG00000113790	NAD+ + 3(S)-3-Hydroxydodecen-(5Z)-Oyl Coenzyme A <=> H+ + NADH + 3-Oxolaur-Cis-5-Enoyl Coenzyme A	ENSG00000072506 or ENSG00000084754 or ENSG00000113790 or ENSG00000133835 or ENSG00000138029 or ENSG00000138796	HSD17B10 or HADHA or EHHADH or HSD17B4 or HADHB or HADH
MAR03297	ENSG00000113790	H2O + Trans,Cis-Dodeca-2,5-Dienoyl Coenzyme A <=> 3(S)-3-Hydroxydodecen-(5Z)-Oyl Coenzyme A	ENSG00000084754 or ENSG00000113790 or ENSG00000127884 or ENSG00000138029	HADHA or EHHADH or ECHS1 or HADHB
MAR03374	ENSG00000113790	trans-2-cis,cis-5,8-tetradecatrienoyl-CoA <=> (3E,5Z,8Z)-Tetradecatrienoyl Coenzyme A	ENSG00000113790 or ENSG00000167969 or ENSG00000198721	EHHADH or ECI1 or ECI2
MAR03378	ENSG00000113790	Trans-2-Cis-8-Tetradecadienoyl Coenzyme A <=> Trans-3-Cis-8-Tetradecadienoyl Coenzyme A	ENSG00000113790 or ENSG00000167969 or ENSG00000198721	EHHADH or ECI1 or ECI2
MAR03379	ENSG00000113790	H2O + Trans-2-Cis-8-Tetradecadienoyl Coenzyme A <=> (3S)-3-Hydroxy-Cis-8-Tetradecenoyl Coenzyme A	ENSG00000084754 or ENSG00000113790 or ENSG00000127884 or ENSG00000138029	HADHA or EHHADH or ECHS1 or HADHB
MAR03380	ENSG00000113790	NAD+ + (3S)-3-Hydroxy-Cis-8-Tetradecenoyl Coenzyme A <=> H+ + NADH + 3-Oxo-Cis-8-Tetradecenoyl Coenzyme A	ENSG00000072506 or ENSG00000113790 or ENSG00000133835 or ENSG00000138796	HSD17B10 or EHHADH or HSD17B4 or HADH
MAR03380	ENSG00000133835	NAD+ + (3S)-3-Hydroxy-Cis-8-Tetradecenoyl Coenzyme A <=> H+ + NADH + 3-Oxo-Cis-8-Tetradecenoyl Coenzyme A	ENSG00000072506 or ENSG00000113790 or ENSG00000133835 or ENSG00000138796	HSD17B10 or EHHADH or HSD17B4 or HADH

Expected feature/value/output:

Remove Peroxisome genes in above table from listed mitochondrial beta-oxidation reactions.

[haowang-bioinfo]

after merging #760, GPRs of MAR03269 and MAR03380 had been resolved and thus excluded from this issue

the changes proposed here to MAR02381 overlap with #759, could thus be implemented together in #770 @Devlin-Moyer ?

[Devlin-Moyer]

oh yea that would work; go ahead

[haowang-bioinfo]

oh yea that would work; go ahead

now all proposed changes in #759 and #767 have been implemented in #770

[haowang-bioinfo]

fixed by #770