Integration tools for SNP-array analysis in variomics

• Grant number: 11/08104-4
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: August 01, 2011
• End date: May 31, 2016
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Ricardo Zorzetto Nicoliello Vêncio
• Grantee: Diego Martinez Salvanha
• Host Institution: Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated scholarship(s): 12/05392-1 - Enabling Gaggle Genome-Browser to variomics research, BE.EP.DD

Abstract

Non-coding RNAs (ncRNAs) are an abundant class of molecules that can act as important elements of gene regulation.Technological advances in molecular biology have helped us to improve the detection of ncRNAs in several organisms, however, the function and structure of most ncRNAs is still unknown. In this project, we propose the application of a systems biology approach, where we integrate multiple sources of high throughput information together with in silico structural predictions of RNAs to identify ncRNAs in the extremophile Halobacterum salinarum NRC-1. The integration of these data classes obtained by experimental and in silico methods in a user-friendly visualization tool allows the users to apply their natural ability to recognize visual patterns on the identification of genomic regions with associated transcript structural evidences. This natural ability in humans can then be used for a better understanding of the studied biological phenomenon. We have thus implemented the Gaggle Genome Browser Web to integrate and visualize large-scale data sets that also allow us to represent secondary structures of RNAs. This new web-tool allowed us to identify 51 new putative ncRNAs so far. The Gaggle Genome Browser web should not only help the identification of new ncRNAs with associated structures but also aid in the study of their role in complex regulatory networks by allowing the integration of multiple data types. (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)

BROOKS, AARON N.; REISS, DAVID J.; ALLARD, ANTOINE; WU, WEI-JU; SALVANHA, DIEGO M.; PLAISIER, CHRISTOPHER L.; CHANDRASEKARAN, SRIRAM; PAN, MIN; KAUR, AMARDEEP; BALIGA, NITIN S.. A system-level model for the microbial regulatory genome. MOLECULAR SYSTEMS BIOLOGY, v. 10, n. 7, JUL 2014. (11/08104-4, 12/05392-1)

BORGES, GISELY T.; VENCIO, ENEIDA F.; QUEK, SUE-ING; CHEN, ADELINE; SALVANHA, DIEGO M.; VENCIO, RICARDO Z. N.; NGUYEN, HOLLY M.; VESSELLA, ROBERT L.; CAVANAUGH, CHRISTOPHER; WARE, CAROL B.; et al. Conversion of Prostate Adenocarcinoma to Small Cell Carcinoma-Like by Reprogramming. Journal of Cellular Physiology, v. 231, n. 9, p. 2040-2047, SEP 2016. (11/08104-4)