Exploration of functional categories in genome-wide expression data has been useful for the discovery of signaling pathways underlying different phenotypes of interest. There are some available tools for the analysis of gene annotations, such as gene ontologies, that allow to examine functional groups of genes in an easy way and to know if their overrepresentation in a given dataset is statistically significant.
A recent paper in Nucleic Acids Research describes a new computational tool to analyze overrepresented chromosomal regions in lists of differentially expressed genes. A freely available web server, called PGE, accepts Ensembl, HGNC or Affymetrix IDs as input and provides a view of significant regions, their P values (including correction for multiple testing) and their respective overrepresentation percentages. This new in silico tool can be very useful for researchers that are trying to correlate global gene expression with specific genomic regions or to find long-range regulators of transcriptional mechanisms.
Author: Katleen De Preter
Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
Reference: De Preter K, Barriot R, Speleman F, Vandesompele J, Moreau Y. Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Res. 2008 Apr;36(7):e43.
Paper available online. The PGE server is available at PGE website.
Message posted by: Diego Forero
Variants Associated with Pediatric Allergic Disorder
Mutations in PHF6 Found in T-Cell Leukemia
Genetic Risk Variant for Urinary Bladder Cancer
Antibody Has Therapeutic Effect on Mice with ALS
Regulating P53 Activity in Cancer Cells
Anti-RNA Therapy Counters Breast Cancer Spread
Mitochondrial DNA Diversity
The Power of RNA Sequencing
‘Pro-Ageing' Therapy for Cancer?
Niche Genetics Influence Leukaemia
Molecular Biology: Clinical Promise for RNA Interference
Chemoprevention Cocktail for Colon Cancer
more news ...