title: bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses.
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
authors: Unité Mixte de Génomique du Cancer, Hôpital Laënnec/Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805 Nantes - Saint Herblain Cedex, France. pascal.jezequel@ico.unicancer.fr
authors: Pascal
authors: P
authors: Jézéquel
authors: Jean-Sébastien
authors: JS
authors: Frénel
authors: Loïc
authors: L
authors: Campion
authors: Catherine
authors: C
authors: Guérin-Charbonnel
authors: Wilfried
authors: W
authors: Gouraud
authors: Gabriel
authors: G
authors: Ricolleau
authors: Mario
authors: M
authors: Campone
mesh_terms: D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics*; D002877:Chromosomes, Human / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm / Q000235:genetics; D006801:Humans; D058977:Molecular Sequence Annotation; D005810:Multigene Family / Q000235:genetics; D009363:Neoplasm Proteins / Q000378:metabolism; D011960:Receptors, Estrogen / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012984:Software; D013223:Statistics as Topic
chemical_list: D009363:Neoplasm Proteins; D011960:Receptors, Estrogen