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BMC Res Notes. 2012 Jun 6;5:265. doi: 10.1186/1756-0500-5-265.

Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.

Author information

  • 1Cryobiology of Stem Cells, Centre of Immunology and Transplantation, Biomedical Research Foundation, Academy of Athens, Soranou Athens, Greece. imichalop@bioacademy.gr

Abstract

BACKGROUND:

Bioinformatics and high-throughput technologies such as microarray studies allow the measure of the expression levels of large numbers of genes simultaneously, thus helping us to understand the molecular mechanisms of various biological processes in a cell.

FINDINGS:

We calculate the Pearson Correlation Coefficient (r-value) between probe set signal values from Affymetrix Human Genome Microarray samples and cluster the human genes according to the r-value correlation matrix using the Neighbour Joining (NJ) clustering method. A hyper-geometric distribution is applied on the text annotations of the probe sets to quantify the term overrepresentations. The aim of the tool is the identification of closely correlated genes for a given gene of interest and/or the prediction of its biological function, which is based on the annotations of the respective gene cluster.

CONCLUSION:

Human Gene Correlation Analysis (HGCA) is a tool to classify human genes according to their coexpression levels and to identify overrepresented annotation terms in correlated gene groups. It is available at: http://biobank-informatics.bioacademy.gr/coexpression/.

PMID:
22672625
[PubMed - indexed for MEDLINE]
PMCID:
PMC3441226
Free PMC Article
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