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

Diego A A Morais; Rita M C Almeida; Rodrigo J S Dalmolin

doi:10.1093/bioinformatics/btz007

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

Bioinformatics. 2019 Aug 15;35(16):2875-2876. doi: 10.1093/bioinformatics/btz007.

Authors

Diego A A Morais¹, Rita M C Almeida², Rodrigo J S Dalmolin^{1

3}

Affiliations

¹ Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
² Institute of Physics and National Institute of Science and Technology: Complex Systems, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
³ Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.

PMID: 30624611
DOI: 10.1093/bioinformatics/btz007

Abstract

Motivation: 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.

Results: 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.

Availability and implementation: http://bioconductor.org/packages/transcriptogramer.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Gene Ontology
Proteins
Software*
Transcriptome

Substances

Proteins