MasterPATH: network analysis of functional genomics screening data

Abstract

Functional genomics employs several experimental techniques to investigate gene functions. These techniques such as loss-of-function screening and transcriptome profiling performed in a high-throughput manner give as result a list of genes involved in the biological process of interest. There exist several computational methods for analysis and interpretation of the list. The most widespread methods aim at investigation of biological processes significantly represented in the list or at extracting significantly represented subnetworks. Here we present a new exploratory network analysis method that employs the shortest path approach and centrality measure to uncover members of active molecular pathways leading to the studied phenotype based on the results of functional genomics screening data. We present the method and we demonstrate what data can be retrieved by its application to the terminal muscle differentiation miRNA loss-of-function screening and transcriptomic profiling data and to the 'druggable' loss-of-function RNAi screening data of the DNA repair process.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

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“…A comprehensive overview of pathway enrichment analysis techniques and the tools that implement them is discussed by [ 7 ]. Recently, Rubanova et al [ 10 ] used a large integrated network of directed and undirected physical and functional relationships between proteins and siRNAs to discover functional paths leading to a phenotype of interest.…”