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. 2013 Jan 15:2013:bas060.
doi: 10.1093/database/bas060. Print 2013.

bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses

Pascal Jézéquel  1 , Jean-Sébastien Frénel, Loïc Campion, Catherine Guérin-Charbonnel, Wilfried Gouraud, Gabriel Ricolleau, Mario Campone
Affiliations

bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses

Pascal Jézéquel et al. Database (Oxford). .

Abstract

We recently developed a user-friendly web-based application called bc-GenExMiner (http://bcgenex.centregauducheau.fr), which offered the possibility to evaluate prognostic informativity of genes in breast cancer by means of a 'prognostic module'. In this study, we develop a new module called 'correlation module', which includes three kinds of gene expression correlation analyses. The first one computes correlation coefficient between 2 or more (up to 10) chosen genes. The second one produces two lists of genes that are most correlated (positively and negatively) to a 'tested' gene. A gene ontology (GO) mining function is also proposed to explore GO 'biological process', 'molecular function' and 'cellular component' terms enrichment for the output lists of most correlated genes. The third one explores gene expression correlation between the 15 telomeric and 15 centromeric genes surrounding a 'tested' gene. These correlation analyses can be performed in different groups of patients: all patients (without any subtyping), in molecular subtypes (basal-like, HER2+, luminal A and luminal B) and according to oestrogen receptor status. Validation tests based on published data showed that these automatized analyses lead to results consistent with studies' conclusions. In brief, this new module has been developed to help basic researchers explore molecular mechanisms of breast cancer. DATABASE URL: http://bcgenex.centregauducheau.fr

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Figures

Figure 1
Figure 1
bc-GenExMiner 3.0 flowchart.
Figure 2
Figure 2
Biological process ontology enrichment results for FTL most positively correlated genes in all patients population (first 15 GO biological process terms).
Figure 3
Figure 3
Detailed results of ESR1 gene expression correlation analysis by chromosomal location for all patients.
Figure 4
Figure 4
Detailed results of LSM1 gene expression correlation analysis by chromosomal location for all patients.
See this image and copyright information in PMC

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