ConsensusGraph: Assessing the Stability of Gene Networks

• Grant number: 15/20897-0
• Support Opportunities: Scholarships in Brazil - Master
• Effective date (Start): December 01, 2015
• Effective date (End): April 30, 2017
• Field of knowledge: Biological Sciences - Immunology - Immunogenetics
• Principal Investigator: Helder Takashi Imoto Nakaya
• Grantee: Pedro de Sá Tavares Russo
• Host Institution: Faculdade de Ciências Farmacêuticas (FCF). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

Systems Biology approaches provide a holistic view of biological processes, integrating the many different molecular components inside cells through highly complex networks. By analyzing these networks, it is possible to create mathematical and computational models that help us understand the molecular mechanisms triggered by different types of stimuli or perturbations. Also, predictive modelling can be applied to reveal gene signatures associated with systemic responses, such as disease outcome or vaccine-induced immunity. However, in addition to the stochasticity of biological processes and the noise associated with high-throughput technologies, gene networks are very dynamic and highly sensitive to changes in conditions and experimental settings. Therefore, studies utilizing the same perturbation with very similar settings and conditions will produce different networks. In my project, we will develop a tool named ConsensusGraph, which will determine a consensus network between independent studies using similar perturbations. We are already refining and testing algorithms that create gene co-expression networks; identify common graphs between networks; and perform functional annotation of gene modules. In order to validate the approach, we will apply ConsensusGraph on 12 HIV studies in order to find differentially expressed genes in the resulting consensus modules. All the code is being written in R and will be freely available to the community.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

RUSSO, PEDRO S. T.; FERREIRA, GUSTAVO R.; CARDOZO, LUCAS E.; BUERGER, MATHEUS C.; ARIAS-CARRASCO, RAUL; MARUYAMA, SANDRA R.; HIRATA, THIAGO D. C.; LIMA, DIOGENES S.; PASSOS, FERNANDO M.; FUKUTANI, KIYOSHI F.; et al. CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. BMC Bioinformatics, v. 19, FEB 20 2018. (15/25825-8, 13/08216-2, 12/19278-6, 14/19323-7, 14/24162-2, 17/05762-7, 15/20897-0)