Question: Significant Biology analysis using differentially expressed genes
0
gravatar for mayurdivate
4.6 years ago by
India
mayurdivate0 wrote:

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.
link: http://www.genmapp.org/go_elite/help_main.htm

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

ADD COMMENTlink modified 4.6 years ago by Manvendra Singh2.1k • written 4.6 years ago by mayurdivate0
0
gravatar for Manvendra Singh
4.6 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

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

ADD COMMENTlink written 4.6 years ago by Manvendra Singh2.1k

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

ADD REPLYlink written 4.6 years ago by mayurdivate0
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