Background This tutorial shows an example of RNA-seq data analysis with DESeq2, followed by KEGG pathway analysis using GAGE. Using data from GSE37704, with processed data available on Figshare DOI: 10.6084/m9.figshare.1601975.

A few weeks ago the 2014 AMIA Translational Bioinformatics Meeting (TBI) was held in beautiful San Francisco.  This meeting is full of great science that spans the divide between molecular and clinical research, but a true highlight of this meeting is the closing keynote, traditionally given by Russ Altman.

Many of you may be familiar with WebGestalt, a wonderful web utility developed by Bing Zhang at Vanderbilt for doing basic gene-set enrichment analyses. Last year, we invited Bing to speak at our annual retreat for the Vanderbilt Graduate Program in Human Genetics, and he did not disappoint! Bing walked us through his new tool called NetGestalt.

I get a lot of requests in the core about running a "pathway analysis." Someone ran a handful of gene expression arrays, or better yet, ran an RNA-seq experiment (with replicates!). These, and many other kinds of high-throughput assays (GWAS, ChIP-seq, etc.) result in a list of genes and some associated p-value, fold change, or other statistic. Here's some R code to download public data from a study on susceptibility to colorectal cancer.

There are several tools available for conducting a post-hoc analysis of GWAS data looking for enrichment of significant SNPs using literature or pathway based resources. Examples include GRAIL, ALLIGATOR, and WebGestalt among others (see SNPath R Package). Since gene enrichment and pathway analysis essentially evolved from methods for analyzing gene expression data, many of these tools require specific gene identifiers as input.

I just read a helpful paper on pathway analysis and interactome reconstruction: Tieri, P., Fuente, A. D., Termanini, A., & Franceschi, C. (2011). Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis. In Bioinformatics for Omics Data, Methods in Molecular Biology, vol.

Vanderbilt Epidemiology Center, Institute for Medicine and Public Health presents: "Pathway-based analysis for genome-wide association studies" Steven Chen Ph.D Assistant Professor of Biostatistics Tuesday, March 16, 2010 9:00 AM - 10:00 AM 2525 West End Avenue 6th Floor BoardroomGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

If you caught Soumya Raychaudhuri's seminar last week you heard a lot about the tool he developed at the broad called GRAIL - Gene Relationships Across Implicated Loci. You've got GWAS results and now you want to prioritize SNPs to follow up in replication or functional studies.

The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in diagrams of pathways, biochemical processes, and cellular processes studied in systems biology.SBGN defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules defining their use and how diagrams are to be interpreted.