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BACA: bubble chArt to compare annotations.

作者信息

Fortino Vittorio, Alenius Harri, Greco Dario

机构信息

Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland.

Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland.

出版信息

BMC Bioinformatics. 2015 Feb 5;16(1):37. doi: 10.1186/s12859-015-0477-4.

DOI:10.1186/s12859-015-0477-4
PMID:25652236
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4377007/
Abstract

BACKGROUND: DAVID is the most popular tool for interpreting large lists of gene/proteins classically produced in high-throughput experiments. However, the use of DAVID website becomes difficult when analyzing multiple gene lists, for it does not provide an adequate visualization tool to show/compare multiple enrichment results in a concise and informative manner. RESULT: We implemented a new R-based graphical tool, BACA (Bubble chArt to Compare Annotations), which uses the DAVID web service for cross-comparing enrichment analysis results derived from multiple large gene lists. BACA is implemented in R and is freely available at the CRAN repository ( http://cran.r-project.org/web/packages/BACA/ ). CONCLUSION: The package BACA allows R users to combine multiple annotation charts into one output graph by passing DAVID website.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e132/4377007/f3734558341b/12859_2015_477_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e132/4377007/dacb441e8c34/12859_2015_477_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e132/4377007/f3734558341b/12859_2015_477_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e132/4377007/dacb441e8c34/12859_2015_477_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e132/4377007/f3734558341b/12859_2015_477_Fig2_HTML.jpg

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本文引用的文献

[1]
RDAVIDWebService: a versatile R interface to DAVID.

Bioinformatics. 2013-8-19

[2]
REVIGO summarizes and visualizes long lists of gene ontology terms.

PLoS One. 2011-7-18

[3]
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis.

Nucleic Acids Res. 2008-7-1

[4]
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

Nucleic Acids Res. 2007-7

[5]
GObar: a gene ontology based analysis and visualization tool for gene sets.

BMC Bioinformatics. 2005-7-25

[6]
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.

Bioinformatics. 2004-11-1

[7]
DAVID: Database for Annotation, Visualization, and Integrated Discovery.

Genome Biol. 2003

[8]
GoMiner: a resource for biological interpretation of genomic and proteomic data.

Genome Biol. 2003

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