No Gene IDs in JPA

MetaboAnalyst
1

Hi all,

I am unsure if there is an error or if it’s something I am doing wrong, but when I enter my transcriptomics data into the Joint Pathway analysis, none of the genes are being identified, using either Uniprot or official gene names. I have over 450 unique identifiers and so I wouldn’t think this was because of unmatched genes? Can you tell me if I might be doing something wrong - here is an example of the genes/uniprot IDs:

MLC5_MOUSE P54357
RLA0_MOUSE P19889
BIP_MOUSE F3YDH0
PDIA6_MOUSE Q9V438
VDAC2_MOUSE Q94920
MYL9_MOUSE P40423
MDHM_MOUSE Q9VEB1
GRP75_MOUSE P29845
FRIS_MOUSE Q9VYH1
GRAN_MOUSE Q11002
TPPP2_MOUSE Q9VV43
MMSA_MOUSE Q7KW39
CATB_MOUSE Q9VY87
MARE1_MOUSE A1Z6P3
TALDO_MOUSE Q9W1G0
ACON_MOUSE Q9VIE8
CROCC_MOUSE Q9VCD1
ITA6_MOUSE Q24247
TAGL_MOUSE Q9VZI1
MPP6_MOUSE M9PDB2
RSSA_MOUSE P38979
AGT2_MOUSE Q95TT3
GELS1_MOUSE Q07171
GDIR1_MOUSE Q9VW59
AL1A1_MOUSE A9J7N9
PDIA3_MOUSE Q9TWZ1
CO6A5_MOUSE Q9VWA7
ADF1_MOUSE P45594
ACTN1_MOUSE M9MS06

Thanks,
Jen

2

Thank you for the question. One possible explanation is that these IDs are not covered by functional annotations - in this case, the KEGG pathways.

Keep in mind that in our enrichment analysis, the background universe is not the whole transcriptome/proteome, but the functionome (pathways, ontologies, gene/metabolite sets). You can find more discussions on this issue here and here

3

Hello,

I had the same problem with Drosophila genes when I used FlyBaseID or official gene names. The only thing that worked was when I used Entrez ID (Entrez Gene: gene-centered information at NCBI - PMC). So may be you could try to convert your IDs into Entrez IDs?

Best regards