Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction.

Abstract

Several freely available tools perform analysis using algorithms developed to identify significant variation of gene expression individually. The transcriptogramer R package uses protein-protein interaction to perform differential expression of functionally associated genes. The software assesses expression profile of entire genetic systems and reveals which biological systems are significantly altered in case-control designed transcriptome experiments. R/Bioconductor transcriptogramer package projects expression values on an ordered gene list to perform topological analysis, differential expression and gene ontology enrichment analysis, independently of data platform or operating system. http://bioconductor.org/packages/transcriptogramer. Supplementary data are available at Bioinformatics online.