Gene Family Anaylsis Tools?

[ZoeG]

Hi, dears,
I am analyzing some RNASeq data.
I have gotten the differential expressed gene lists, which have hundreds or thousands of genes.
Studying them one by one is just time-consuming and low efficient.
So I am thinking about pathway analysis and gene family analysis.
I just searched, but didn't find specific tools for gene family analysis.
Do you know any available tools for gene family analysis?
Thank you.

[JackieBadger]

Be specific in what you mean by gene family analysis

[ZoeG]

Be specific in what you mean by gene family analysis

Most basically, for a given gene list from one species, the analysis can assign the genes to its corresponding gene family, so we can easily group the genes by its gene family. More details such as the chromosome, the loci, its function are better.
An across species analysis would be great.

[sphil]

Hi,

maybe you wanna check out something like this http://www.bioconductor.org/help/cou...008/labs/GSEA/ which gives you a statistical significance on the way. Else you might want to look for blast2go or any other GO-Term related tool.

Cheers

[JackieBadger]

and this http://prospectus.usherbrooke.ca/cluss/

[ZoeG]

Thanks, sphil.
This tool seems interesting.
Try to dig it and see whether it could be used for gene family.

Hi,

maybe you wanna check out something like this http://www.bioconductor.org/help/cou...008/labs/GSEA/ which gives you a statistical significance on the way. Else you might want to look for blast2go or any other GO-Term related tool.

Cheers

[ZoeG]

Hi, Jackie,
a little confused. Isn't it an aligner for protein?

and this http://prospectus.usherbrooke.ca/cluss/

[JackieBadger]

Yup.

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013409

[ZoeG]

Nice paper! Thanks, Jackie

Yup.
http://www.plosone.org/article/info:...l.pone.0013409

[jp.]

I read the above post and got to ask, if somebody can tell me how can I do pathway analysis with diff_gene values... is there any free tools...
thanks in advance

[ZoeG]

I read the above post and got to ask, if somebody can tell me how can I do pathway analysis with diff_gene values... is there any free tools...
thanks in advance

Hi, jp, I am using AltAnalyze which is an open-source free tool.

[jp.]

Thank you for your reply
Its is for alt splicing ?
Anything for diff_genes ?

Hi, jp, I am using AltAnalyze which is an open-source free tool.

[ZoeG]

Thank you for your reply
Its is for alt splicing ?
Anything for diff_genes ?

This software can do differential gene expression, alt splicing and also allow you to do pathway analysis.