title: Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data.
abstract: Systemic approaches are essential in the discovery of disease-specific genes, offering a different perspective and new tools on the analysis of several types of molecular relationships, such as gene co-expression or protein-protein interactions. However, due to lack of experimental information, this analysis is not fully applicable. The aim of this study is to reveal the multi-potent contribution of statistical network inference methods in highlighting significant genes and interactions. We have investigated the ability of statistical co-expression networks to highlight and prioritize genes for breast cancer subtypes and stages in terms of: (i) classification efficiency, (ii) gene network pattern conservation, (iii) indication of involved molecular mechanisms and (iv) systems level momentum to drug repurposing pipelines. We have found that statistical network inference methods are advantageous in gene prioritization, are capable to contribute to meaningful network signature discovery, give insights regarding the disease-related mechanisms and boost drug discovery pipelines from a systems point of view.
authors.affiliation: Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece.|Department of Informatics and Telecommunications, University of Athens, 15784 Ilissia Athens, Greece.
authors.forename: Marilena M
authors.initials: MM
authors.lastname: Bourdakou
authors.affiliation: Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece.
authors.forename: Emmanouil I
authors.initials: EI
authors.lastname: Athanasiadis
authors.affiliation: Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece.
authors.forename: George M
authors.initials: GM
authors.lastname: Spyrou
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001943:Breast Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D019295:Computational Biology; D030541:Databases, Genetic; D004843:Epistasis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D053263:Gene Regulatory Networks; D006801:Humans; D009367:Neoplasm Staging; D016571:Neural Networks, Computer; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000187:drug effects
chemical_list: D000970:Antineoplastic Agents