[BUG] Mitochondrial genes are missing in gene ontology analysis

[Dragonmasterx87]

Describe the bug Thank you for creating EnrichR! I have noticed that when adding human mitochondrial genes they do not generate gene ontologies, for example, GO:0031966. Could you please include the 13 human mitochondrial genes? Such as MT-##? Is there a different gene name than MT-## (## being different for each of the 13 gene names such as MT-CO3)

To Reproduce Steps to reproduce the behavior:

1. Go to 'EnrichR'
2. Add mitochondrial gene lists
3. No gene ontology information such as cellular component, biological process or molecular function

Expected behavior A populated Gene ontology list should be available.

Desktop (please complete the following information):

• OS: Windows 10, ubuntu
• Browser chrome

Thanks!!

[AviMaayan]

We do not have strict rules about the supported gene symbols, so it is possible that for these genes older names will return better results. For example, MT-CO3 is also known as COX3 which is supported by some Enrichr libraries: https://maayanlab.cloud/Enrichr/#find!gene=COX3

[Dragonmasterx87]

Thanks Avi! I do notice that the GO terms still don't come populated for corresponding mitochondrial genes, however, KEGG and wikipathways are populated.

[Dragonmasterx87]

Sorry to re-open this issue, but I have had to shift to another GO tool because EnrichR doesn't take into account mitochondrial genes. I have tried different gene notations, including COX3 as opposed to the MT-COX3 but still this yields no gene ontology information. For example, in cells have upregulated mitochondrial encoded genes:

MT-ATP6 (ATP synthase 6) MT-ATP8 (ATP synthase 8) MT-CO1 (cytochrome c oxidase subunit 1) MT-CO2 (cytochrome c oxidase subunit 2) MT-CO3 (cytochrome c oxidase subunit 3) MT-CYB (cytochrome b) MT-ND1 (NADH dehydrogenase subunit 1) MT-ND2 (NADH dehydrogenase subunit 2) MT-ND3 (NADH dehydrogenase subunit 3) MT-ND4 (NADH dehydrogenase subunit 4) MT-ND4L (NADH dehydrogenase subunit 4L) MT-ND5 (NADH dehydrogenase subunit 5) MT-ND6 (NADH dehydrogenase subunit 6) MT-RNR1 (12S ribosomal RNA) MT-RNR2 (16S ribosomal RNA) MT-TA (tRNA-Ala) MT-TC (tRNA-Cys) MT-TD (tRNA-Asp) MT-TE (tRNA-Glu) MT-TF (tRNA-Phe) MT-TG (tRNA-Gly) MT-TH (tRNA-His) MT-TI (tRNA-Ile) MT-TK (tRNA-Lys) MT-TL1 (tRNA-Leu1) MT-TL2 (tRNA-Leu2) MT-TM (tRNA-Met) MT-TN (tRNA-Asn) MT-TP (tRNA-Pro) MT-TQ (tRNA-Gln) MT-TR (tRNA-Arg) MT-TS1 (tRNA-Ser1) MT-TS2 (tRNA-Ser2) MT-TT (tRNA-Thr) MT-TV (tRNA-Val) MT-TW (tRNA-Trp) MT-TY (tRNA-Tyr)

I haven't been able to detect gene ontologies. For example, using cytoscape or R wrappers for GO, profiler, topGO, clusterprofileR, one can detect mitochondrial ETC gene regulated pathways such as Aerobic respiration or ATP production via ETC, but for some reason EnrichR's online portal doesn't recognize these genes.

Would love for someone to look into this, I'm sure its an ez fix.

Thanks!

🐉

[Dragonmasterx87]

Upon doing some diging I notice that for the appended gene notation such as COX3, the Gene ontology terms are missing. Which is a bug, because the GO terms are more expansive over the HPO terms.