BART: bioinformatics array research tool

Abstract

BackgroundMicroarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and requires manual error-prone analysis and a bioinformatics background. This is due to a lack of standardization in array platform fabrication as well as the lack of a simple interactive tool for clustering, plotting, differential expression testing, and testing for functional enrichment.ResultsWe introduce the Bioinformatics Array Research Tool (BART), an R Shiny web application that automates the microarray download and analysis process across diverse microarray platforms. It provides an intuitive interface, automatically downloads and parses data from GEO, suggests groupings of samples for differential expression testing, performs batch effect correction, outputs quality control plots, converts probe IDs, generates full lists of differentially expressed genes, and performs functional enrichment analysis. We show that BART enables a more comprehensive analysis of a wider range of microarray datasets on GEO by comparing it to four leading online microarray analysis tools.ConclusionsBART allows a scientist with no bioinformatics background to extract knowledge from their own microarray data or microarray experiments available from GEO. BART is functional on more microarray experiments and provides more comprehensive analyses than extant microarray analysis tools. BART is hosted on bart.salk.edu, includes a user tutorial, and is available for download from https://bitbucket.org/Luisa_amaral/bart.

Transcriptomics & copy number variation of radiotoxicity points to altered mitochondrial and DNA repair mechanisms

“…Further details of the study have been described elsewhere [24]. We analyzed differentially expressed genes between groups receiving 0Gy and 2 Gy of radiation using BART [25] and NCBI's GEO2R. We tested the significance of genes overlapping our results from prostate and whole-blood tissue to those identified in the replication dataset using GeneOverlap…”

Genetically-regulated transcriptomics & copy number variation of proctitis points to altered mitochondrial and DNA repair mechanisms in individuals of European ancestry

“…Further details of the study have been described elsewhere [24]. We used BART [25] and NCBI's GEO2R to analyze differentially expressed genes between untreated and treated with 2 Gy of radiation groups. .…”

Genetically-regulated transcriptomics & copy number variation of proctitis points to altered mitochondrial and DNA repair mechanisms in individuals of European ancestry

“…Further details of the study have been described elsewhere [24]. We used BART [25] and NCBI's GEO2R to analyze differentially expressed genes between untreated and treated with 2 Gy of radiation groups. We tested the signi cance of genes overlapping our results from prostate and whole-blood tissue to those identi ed in the replication dataset using GeneOverlap (https://github.com/shenlab-sinai/geneoverlap) which applies Fisher's exact test testing signi cant genes for whole blood tissue (n=98), prostate tissue (n=62) and replication cohort (n=2973) against genome (n=21196) .…”