Joel P Arrais1, João Fernandes, João Pereira, José Luís Oliveira. 1. Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal.
Abstract
BACKGROUND: The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible. RESULTS: GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways. CONCLUSIONS: GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.
BACKGROUND: The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible. RESULTS: GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways. CONCLUSIONS: GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.
Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock Journal: Nat Genet Date: 2000-05 Impact factor: 38.330
Authors: Sorin Draghici; Purvesh Khatri; Pratik Bhavsar; Abhik Shah; Stephen A Krawetz; Michael A Tainsky Journal: Nucleic Acids Res Date: 2003-07-01 Impact factor: 16.971
Authors: Andrea L Richardson; Zhigang C Wang; Arcangela De Nicolo; Xin Lu; Myles Brown; Alexander Miron; Xiaodong Liao; J Dirk Iglehart; David M Livingston; Shridar Ganesan Journal: Cancer Cell Date: 2006-02 Impact factor: 31.743
Authors: Barry R Zeeberg; Weimin Feng; Geoffrey Wang; May D Wang; Anthony T Fojo; Margot Sunshine; Sudarshan Narasimhan; David W Kane; William C Reinhold; Samir Lababidi; Kimberly J Bussey; Joseph Riss; J Carl Barrett; John N Weinstein Journal: Genome Biol Date: 2003-03-25 Impact factor: 13.583
Authors: Misha Kapushesky; Ibrahim Emam; Ele Holloway; Pavel Kurnosov; Andrey Zorin; James Malone; Gabriella Rustici; Eleanor Williams; Helen Parkinson; Alvis Brazma Journal: Nucleic Acids Res Date: 2009-11-11 Impact factor: 16.971
Authors: Charles W Rehrer; Anis Karimpour-Fard; Teri L Hernandez; Christopher K Law; Nichole R Stob; Lawrence E Hunter; Robert H Eckel Journal: Obesity (Silver Spring) Date: 2012-05-04 Impact factor: 5.002
Authors: Miguel Reboiro-Jato; Joel P Arrais; José Luis Oliveira; Florentino Fdez-Riverola Journal: BMC Bioinformatics Date: 2014-01-30 Impact factor: 3.169