Seten: A tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles

Abstract

RNA-binding proteins (RBPs) control the regulation of gene expression at posttranscriptional level. Several CLIP (crosslinking and immunoprecipitation) protocols are available to study RBPs; however, there are very few tools to understand gene set associations of them. We developed Seten to help identify and compare processes, phenotypes and diseases associated with RBPs. After detection of peaks, they can be given as BED files or gene - score pairs to Seten for this analysis. The peak scores reflect the extent of binding of an RBP on the target transcript, which can be used to do a gene set enrichment analysis. Seten provides a gene set enrichment and functional enrichment methods including pathways, Gene Ontology, phenotypes and diseases gene set collections for a number of organisms. Seten has a web (JavaScript) and command line (Python) interface. Seten web interface provide several visualization options for identification and comparison of results. Seten command line interface can be used to analyze multiple datasets. We also provide precomputed results for more than 200 CLIPseq datasets from CLIPdb and ENCODE peak-detected datasets.