Population-based meta-heuristic for active modules identification

Leandro Corrêa 1 Denis Pallez 1 Laurent Tichit 2 Olivier Soriani 3 Claude Pasquier 1
1 Laboratoire I3S - SPARKS - Scalable and Pervasive softwARe and Knowledge Systems
2 AMU SCI - Aix-Marseille Université - Faculté des Sciences
3 IBV - Institut de Biologie Valrose
Abstract : The identification of condition specific gene sets from transcriptomic experiments has important biological applications, ranging from the discovery of altered pathways between different phenotypes to the selection of disease-related biomarkers. Statistical approaches using only gene expression data are based on an overly simplistic assumption that the genes with the most altered expressions are the most important in the process under study. However, a phenotype is rarely a direct consequence of the activity of a single gene, but rather reflects the interplay of several genes to perform certain molecular processes. Many methods have been proposed to analyze gene activity in the light of our knowledge about their molecular interactions. We propose, in this article, a population-based meta-heuristics based on new crossover and mutation operators. Our method achieves state of the art performance in an independent simulation experiment used in other studies. Applied to a public transcriptomic dataset of patients afflicted with Hepatocellular carcinoma, our method was able to identify significant modules of genes with meaningful biological relevance.
Keywords : Evolutionary algorithms Transcriptomics Biological networks
Document type :
Conference papers
Complete list of metadatas
https://hal.archives-ouvertes.fr/hal-02366236
Contributor : Claude Pasquier <>
Submitted on : Friday, November 15, 2019 - 5:42:04 PM
Last modification on : Saturday, November 16, 2019 - 1:42:33 AM

Identifiers

  • HAL Id : hal-02366236, version 1

Collections

I3S | CNRS | UNICE | UNIV-COTEDAZUR | UNIV-AMU

Citation

Leandro Corrêa, Denis Pallez, Laurent Tichit, Olivier Soriani, Claude Pasquier. Population-based meta-heuristic for active modules identification. 10th International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2019), Dec 2019, Nice, France. ⟨hal-02366236⟩

Export

BibTeX TEI DC DCterms EndNote

Share

Metrics

Record views

17

Contact

Informations

CCSD