Differential Expression Analysis: Finding Genes that Matter

This will start with a brief introduction to differential expression analysis. This is the approach of comparing gene expression in two or more tissue samples to compare the way genes are expressed in various conditions. This will cover the basic principle, caveats, and a couple different approaches.

The second part will focus on one particular method for expression analysis, as developed by the Pachter Lab at UC Berkeley. They have used a newer method of assigning RNA-Seq reads to the correct locations of the genome. The RNA-Seq quantification is handled by the program kallisto, and the differential expression is performed by sleuth.

Web Pages for the tools:

http://pachterlab.github.io/kallisto/about.htm (http://pachterlab.github.io/kallisto/about.html)l

http://pachterlab.github.io/sleuth/about.html

The paper itself:

http://arxiv.org/pdf/1505.02710v2.pdf