The integration of Pathway Analysis into genomic data analysis

Question

[nina]

Hi, Does anyone have any advice for the integration of pathway analysis into sequencing data analysis such as WGS or WES data? I am new in pathway analysis and I want to find the way to use pathway analysis result to prioritise SNPs related diseases. Thank you.

Answer 1

[cordelia.ziraldo]

Hi Nina,

There are a few common approaches, and they all start by processing your sequence data to generate a VCF file of variants. Then, to get from variants to pathway analysis there are just a few steps:

1. apply QC filters to keep only variants you believe are there;
2. define your set of high-priority variants. There are many ways to do this; it depends on your experiment. (Rare? Homozygous? Common in cases but rare in controls? Predicted to be deleterious? previously identified as significant, etc etc)
3. Map the set of high-priority variants to impacted genes and perform enrichment analysis on pathways.

There are a few tools out there that help with these steps. iVariantGuide is a new one that has a clean interface that's very graphical/ interactive. And it automatically generates a PDF report for you. In addition to pathways, it lets you do GO analysis on your variant sets, too. You can see how it all works on the demo analysis that comes with your account. It's a commercial tool, but it's free to upload your VCF, annotate it, and use the filters.