GO analysis using GO IDs

Question

[friasoler]

Hello everybody I'm doing some transcriptomic analysis from a non-model organism, a migratory bird. We have used the zebra finch & turkey genome and the uniprot & NCBI databases for the annotation. In consequence the annotated genes come from many different organisms (zebra finch, turkey, humans, mouse.....etc). Using this list of genes (Uniprot IDs) I can get their GO Ids; but I cant perform a GO analysis because most of the tools need to choose a single organism to match the gene list. Any time I want to translate my genes to any other species I lost information because not all genes have an orthologous, that imply a bias in the data interpretation. Is there anytool that uses GOids for an enrichment analysis? Have you any suggestion how to deal with that issue? I will appreciate any help you can give me Thanks in advance A short example of the list Im dealing with: UD16_HUMAN PUR6_CHICK MCFD2_RAT UK114_HUMAN PUR1_CHICK TDH_BOVIN

[Alex]

maybe you can send the data to me and I can help you

[friasoler]

Hello Alex Thanks a lot for the offer...should we talk by email? LG RC

[Alex]

Hi ,friasoler I'm sorry to reply you at this moment ,if you have trouble in GO analysis ,you can send a email to me [e-mail]

[vetsfindkhes]

Hi Alex, I am having this issue, Can you help me? Thanks.

Answer 1

[h.mon]

As you created your own transcript to GO mapping, you could use GAGE or CAMERA - both Bioconductor packages - to perform enrichment analysis.