Retrieval and analysis of gene annotation is now a central step in many genomic workflows. There is a large number of independent online resources that provide detailed annotations for specific categories. Thus, there is a clear need for centralized resources that facilitate integrated analyses.
A recent paper in Genome Biology describes BioGPS, a freely available online resource that provides a centralized gene annotation portal. BioGPS, developed by Andrew Su et al, gives the opportunity of visualizing additional gene annotation resources as plugin layers. There are more than 150 available plugins and some categories are: Literature Search (PubMed, Google Scholar), Gene Portals (Ensembl, GeneCards), Genetics (dbSNP, HapMap), Pathway Tools (KEGG, STRING) and Reagent Providers. Users can register and customize their plugin profiles.
The main primary resource at BioGPS is the Gene Atlas/SymAtlas, a highly cited and used online tool that provides detailed gene expression data for humans and mice in a large number of tissues and cells.
BioGPS uses a platform that allows for the easy and fast integration of further resources. It is expected that BioGPS and similar resources will allow faster and easier integrated analyses of genomics data, such as those coming from genome-wide expression and association studies.
On this 2010, I will keep writing about further papers and tools of interest, continuing with this useful international bridge between bioinformatics / computational biology and human genetics / genomics (and it is free). Stay tuned.
Andrew Su, PhD
Computational Biology Group, Genomics Institute of the Novartis Research Foundation, San Diego, USA.
Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 2009 Nov 17;10(11):R130. Freely available full text paper.
Prof. Dr. Diego A. Forero, MD, PhD
Message posted by: Diego Forero