Best Methods for Measuring the similarity of two pairwise Gene Expression contrasts
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4.7 years ago
adam.faranda ▴ 110

In a recent RNA Sequencing experiment, we've identified a set of genes with Pax6 dependent differential expression in the cornea. Initial evaluation of this signature suggests that in Pax6 mutants, corneal tissues begin to adopt a conjunctival phenotype. We've found an existing data set that provides expression profiles for both tissues (cornea and conjunctiva), and would like to compare our Pax6 signature to this data. Genes that up-regulate in the absence of Pax6 also tend to up-regulate in the the conjunctiva (vs cornea). Likewise, genes that down-regulate in the absence of Pax6 tend to down-regulate in the conjunctiva. Is there one or more recommended statistical methods for quantifying the extent to which conjuctiva-specific genes are reflected in our Pax6 signature?

RNA-Seq microarray differential expression • 723 views
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This sounds like a job for Gene Set Enrichment Analysis, using this Pax6 signature as a custom gene set. See http://software.broadinstitute.org/gsea/index.jsp

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