Integrative analysis of differential gene expression to elucidate molecular mechanisms that control meat tenderness in Nellore cattle

• Grant number: 13/26121-9
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Start date: March 01, 2014
• End date: June 30, 2014
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Luiz Lehmann Coutinho
• Grantee: Tassia Mangetti Gonçalves
• Supervisor: James M. Reecy
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Institution abroad: Iowa State University, United States
• Associated to the scholarship: 12/23934-6 - Differential expression of genes related with meat tenderness in nelore cattle, BP.MS

Abstract

Systems biology studies can be used together with gene expression analysis to provide a better understanding of the dynamic interactions that occur between genes. The large number of different cellular processes may be getting a reductionist approach by having deficiencies in analyzes that hinder the interpretation of many genes and their difference of connectivity. Many researchers have developed programs that analyze complex networks for better understanding of systems biology. To understand the biological process of meat tenderness, integrative analysis is advantageous to unravel the usefulness of all the genes identified in the survey. The proposal of this project is give an approach to the integration of networks that generate a number of possible models that explain the activity of transcriptional regulation. Methods based on the study of transcription factors (TF) were developed because they play important regulatory role in the control of gene expression, showing the absolute mean of correlation of co-expression of all genes. The algorithm regulatory impact factor (RIF) studies the functional activation of TF. The PCIT (Partial Correlation Information Theory), a more sensitive method, gives the difference in behaviour or specific co-expression of target gene pairs and performs the quantification of differential gene connectivity. The study that shows the importance of each differentially gene expressed in the phenotype in the change is the phenotypic impact factor (PIF). The use of the PCIT, RIF and PIF analyzes will help us to elucidate the process of meat tenderness. (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)

GONCALVES, TASSIA MANGETTI; DE ALMEIDA REGITANO, LUCIANA CORREIA; KOLTES, JAMES E.; MELLO CESAR, ALINE SILVA; DA SILVA ANDRADE, SONIA CRISTINA; MOURAO, GERSON BARRETO; GASPARIN, GUSTAVO; MONTEIRO MOREIRA, GABRIEL COSTA; FRITZ-WATERS, ELYN; REECY, JAMES M.; et al. Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle. FRONTIERS IN GENETICS, v. 9, OCT 5 2018. (13/26121-9, 12/23934-6)