Development of a bioinformatics strategy to search for genes involved in specific metabolic pathways: The case of ESCs.

ROHR, CRISTIAN; PARRA, RODRIGO GONZALO; GALIAN, EVANGELINA; YANKILEVICH, PATRICIO; PEREZ CASTRO, CAROLINA

Córdoba

Congreso; II Congreso Argentino de Bioinformática y Biología Computacional; 2011

Facultad de Ingeniería de la Universidad Católica de Córdoba

The study of transcriptional networks involved in various metabolic pathways is fundamental to understand the cellular response. We have developed a strategy based on the use of bioinformatics tools currently available (Biomart, RSATools, DAVID), along with scripts generated by the authors. This strategy was applied to on a systematic search for genes potentially involved in the pluripotent state of embryonic stem cells (ESCSs), determining the possible consensus binding sites for different transcription factors (TFs), Oct4[1], Sox2[2] and Nanog[3], together with complemented analysis of these sites in orthologous genes from different species. Using previously published experimental data (microarray, ChIP on ChIP-and reporter vector) [5], we tested our scripts prediction potential analyzing for the presence of consensus sequences corresponding to these TFs in silico and compared to the real data. Following a comparative analysis between different species, we generated a list of genes including previously reported genes and promise new candidates genes that are potentially regulated by TFs in pluripotent cells. We propose our script is an interesting systematic tool for use in the study of mammalian cell transcriptional networks.