ConsensusGraph: identifying consensus gene networks

• Grant number: 17/05762-7
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Effective date (Start): July 01, 2017
• Effective date (End): April 30, 2019
• Field of knowledge: Biological Sciences - Immunology - Immunogenetics
• Principal Investigator: Helder Takashi Imoto Nakaya
• Grantee: Pedro de Sá Tavares Russo
• Host Institution: Instituto de Matemática e Estatística (IME). 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. However, even very similar studies can produce different networks. Therefore, there is a need to integrate the different information conveyed in each network in a robust manner, in order to provide new insights into the underlying biological mechanisms. In this project, we will develop a tool named ConsensusGraph, which will determine a consensus network between independent studies using similar perturbations. Our group has already described a tool that creates gene co-expression networks and performs functional annotation of gene modules, and we will use it to provide the networks to be combined. In order to validate the approach, we will apply ConsensusGraph on public transcriptomics datasets 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. (AU)

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)

CARDOZO, LUCAS E.; RUSSO, PEDRO S. T.; GOMES-CORREIA, BRUNO; ARAUJO-PEREIRA, MARIANA; SEPULVEDA-HERMOSILLA, GONZALO; MARACAJA-COUTINHO, VINICIUS; NAKAYA, I, HELDER. webCEMiTool: Co-expression Modular Analysis Made Easy. FRONTIERS IN GENETICS, v. 10, MAR 6 2019. (13/08216-2, 17/05762-7, 18/10748-6, 12/19278-6)

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)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

RUSSO, Pedro de Sá Tavares. Development of a computational tool for gene co-expression analyses and its application in systems biology. 2019. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.