Illumina Exome Chip And Pathway Analysis

Question

[alizaid12]

Hi there. I am writing after reviewing Biostar threads for information on pathway analysis. I could not find relevant answers on exome data in the context of pathway analysis (after mapping exome data to genes and then to relevant pathways)

I have also used DAVID and managed to get pathway maps in KEGG (but this only displays genes of significance without precisely identifying the relative signifance of p-values for the genes in the pathway)..and

I have used Webgestalt-v2 (Vanverbilt University) and PLINK for SNP-based pathway analysis before. These utilities worked beautifully, but I used for SNP-pathway analysis. Especially, Webgestalt-v2 allows input of SNP data by p-values, which can be used to trace the signifiance of genes within pathways, as well

At this time...

After reading some papers and also examining tutorials for atleast 3 softwares (GenGen, GSEA and Gene Pattern), I could not identify relevant points related to exome data and pathway analysis.

I would be very grateful if someone could share their experience in this regards. I can ofcourse, immmediately proceed to work with some of the above identified softwares but if there are other recommended softwares / utilities, then I would give them priority.

Thankyou in advance for a reply

Ali

[Sean Davis]

What is the biologic setting? Tumor/normal, case-control, mendelian trait?

Answer 1

[alizaid12]

Hi there

Thanks a bunch for your response and my apologies for a belated reply. With regards to your query, I provide the following information a) Regrading biologic setting; The data is case-control b) Regarding chip type; Illumina Infinium HumanExome BeadChip (48 samples) c) Regarding the method of analysis; We used in house scripts in R to perform genotyping

If any further information would assist in solving my issue, please feel free to inquire. I appreciate your consideration and time to help solutions for this work.

Regards

Miki