IsopretGO: Isoform interpretation

IsopretGO (Isoform Interpretation for Gene Ontology) leverages predictions of isoform-specific functions (i.e., Gene Ontology[GO] annotations) made by the isopret expectation maximization algorithm. to perform gene-level and isoform-level GO overrepresentation analysis.

Background: Gene Ontology

Gene Ontology. traditionally has provided annotations for genes rather than for specific isoforms. However, in some cases, the functions of the individual isoforms of a gene are differ with respect to one or more of the gene's function. In this project, we have developed an algorithm for prediction of isoform-specific function across the entire transcriptome. The isopret app offers a number of ways to visualize and analyze RNA-seq datasets for Gene Ontology functions that are overrepresented either among the differentially expressed genes or the differentially spliced isoforms.

Background: HBA-DEALS

Isopret requires as input a file that has the fold changes and p-values for genes and isoforms in a case-control cohort that has been studied by RNA-seq. We have previously published HBA-DEALS., a hierarchical Bayesian algorithm that performs such an analysis, and this is the recommended input file. Isopret uses the analysis (output) file of HBA-DEALS.

HBA-DEALS analyzes RNA-Seq data to determine differentially expression and differential splicing simultaneous. Isopret then performs Gene Ontology analysis using an updated implementation of code from the Ontologizer.