Significant Biology analysis using differentially expressed genes

Question

[mayurdivate]

Hello everyone,

Best wishes.

I want find out statistically significant pathway and gene ontology of miRNAs annotation of deep sequencing data.

I have annotated known and Novel miRNAs. Based on annotation, Is there any method to find significant pathways and GOs ?

One I know is GoElite by gladstone institute.

but with this I am not getting any significant GOs and Pathways.

If you have done significant biology analysis or heard about any tool please let me know.

Thanks

Answer 1

[Manvendra Singh]

for me, Gene Ontologies are that you always get something relative what you are looking for.

For miRNA, I would suggest you to try GOmir, its quite strong and trustable.

http://www.bioacademy.gr/bioinformatics/GOmir/bioinformatics_home.htm

HTH

[mayurdivate]

Hello Manu,

Thanks for your reply.

I have both known and novel miRNAs in differential list. So I want know which GOS and Pathways are statistically significant from differential list as compare to total expressed miRNAs. Statically significant means as per z-score, p-value etc.

So that number of GOs and pathways will get reduced to few.

I do not know much about GOmir. I am looking into it. If you have used it before, please tell can it be used for my purpose ?

Thanks
Mayur