Downstream analysis for Differential Expression..

[papori]

Hi folks!

We did De novo RNASeq for invertebrate transcriptome.
We had 3 biological conditions.
I found that a list of 150 contigs are differentially expressed between all the conditions.(I used DESeq of R)
i blastx those contigs against uniprot to get some homologous information.
Is there any recommended tool for downstream analysis?

Thanks,
Pap

[papori]

Ok,
Maybe i wasn't clear enough..
When i said Downstream analysis i meant to GO annotate, KEGG.. For getting more information about my contigs.
As far, i found Blast2GO..

Any help will be appreciate!
Thanks,
Pap

[Hobbe]

Blast2GO is great. I think you will be very happy with the results.

[pbluescript]

Here are a couple alternatives to Blast2GO.

Since you have experience in R, you could try GoSeq.

http://www.bioconductor.org/packages/2.6/bioc/html/goseq.html

Or you could try DAVID, which simply requires a list of genes. I like the output format it produces.

http://david.abcc.ncifcrf.gov/

[rpeters]

Partek provides a host of integrated downstream tools including gene set enrichment analysis, GO Enrichment, KEGG Enrichment, etc. For a more comprehensive view into gene set analysis using more powerful statistics, gene set ANOVA or pathway ANOVA can be used to look at multiple factors influencing differentially expressed functional groups or pathways, as well as uncover genes that express differently in the pathway or functional group based on different conditions. The ANOVA analysis will pick up gene sets and pathways missed by other basic gene set analysis that merely looks at presence of genes in specific groups.

For differential expression of genes/transcripts, I would also like to mention, that Partek has a Gene Specific Analysis where each gene/transcript can be analyzed independently and fit to the best model based on its distribution (Poisson, Neg. Binomial, Log Normal), and better understand which factors are influencing the expression.

[papori]

What is Partek?
Can you share the link please?
Thanks,

[rpeters]

Partek creates software for the analysis of Microarray and Next Generation Sequencing data with an emphasis on statistical analysis and visualizations.

http://www.partek.com/

[papori]

Blast2GO is great. I think you will be very happy with the results.

Can i work with Blast2Go from commandline? Not GUI..?
Otherwise it can take forever..
Thanks..

[westerman]

Blast2go has a command line tool called b2g4pipe. Look at the web site. B2g4pipe does not do everything that the GUI does but b2g4pipe can create the *.dat file much more quickly than the GUI and once you have the *.dat file then the rest of the processing becomes quick.

[papori]

Thanks westerman!
i will go for it..