Bioinformatics Seminar
Time:
Venue: Na
12 June 2018
NaFRY: A fast and accurate approach to identifying biological pathways
Goknur GinerWEHI Bioinformatics
Gene set tests help researchers identify significantly enriched biological pathways in the concept of differential expression. A plethora of methods in the literature differs in many aspects. Most gene set tests permute gene labels to evaluate p-values. Such calculation ; however ; assumes independence of genes and can inflate the false discovery rate even for small correlations. To keep the correlation structure unchanged we can permute the samples instead of genes ; yet this method can only be used with simple experimental designs with a few replicates. To overcome aforementioned limitations ; one of the most flexible ; powerful and robust gene set tests is ROAST in limma package. ROAST uses residual space rotation as a sort of continuous version of sample permutation. Like permutation tests ; it protects against false positives caused by correlations between genes in the set. Unlike permutation tests ; it is applicable to all designs.
This talk will cover the different statistical approaches to popular gene set analysis pipelines and present the gene set test FRY in detail. FRY is a very fast approximation to the complete ROAST method. FRY preserves most of the advantages of ROAST but also provides high-resolution exact p-values very quickly. In particular ; it is able to distinguish the most significant sets in large collections and to yield statistically significant results after adjustment for multiple testing.