Question: GO analysis using GO IDs
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gravatar for friasoler
3.0 years ago by
friasoler20
Germany
friasoler20 wrote:

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

rna-seq go ids gene ontology • 1.2k views
ADD COMMENTlink modified 3.0 years ago by h.mon28k • written 3.0 years ago by friasoler20

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

ADD REPLYlink written 3.0 years ago by Alex30

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

ADD REPLYlink written 3.0 years ago by friasoler20

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 zhongweimin63@gmail.com

ADD REPLYlink written 3.0 years ago by Alex30
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gravatar for h.mon
3.0 years ago by
h.mon28k
Brazil
h.mon28k wrote:

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

ADD COMMENTlink written 3.0 years ago by h.mon28k
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