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

BMC Research Notes

Sophia Kossida⁴  Reinhard Schneider²  Myrto-Areti Kostadima⁴  Alexandros Karelas³  Apostolos Malatras¹  Georgios A Pavlopoulos⁵  Ioannis Michalopoulos³ 

[1]Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, 15701, Greece

[2]Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, avenue des Hauts-Fourneaux 7, Esch sur Alzette, L-4362, Luxembourg

[3]Cryobiology of Stem Cells, Centre of Immunology and Transplantation, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens, 11527, Greece

[4]Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens, 11527, Greece

[5]ESAT-SCD/IBBT-K.U. Leuven Future Health Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Heverlee-Leuven, 3001, Belgium

关键词: Functional annotation;    Gene coexpression;    Gene annotation;    Microarray analysis;   

Others  :  1166376
DOI  :  10.1186/1756-0500-5-265

 received in 2011-12-24, accepted in 2012-05-24,  发布年份 2012

【 摘 要 】

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/ webcite.

【 授权许可】

   
2012 Michalopoulos et al.: licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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