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

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

Simposio; Frontiers in BioScience; 2012

Polo Científico Tecnológico- Buenos Aires-Argentina

In previous work, we identified potential genes to be involved in the regulation of embryonic stem cells (ESCs) properties, using several bioinformatic tools and house-made scripts. We developed algorithms to search for a group of transcription factors binding sites (TFBSs) corresponding to the ESCs transcriptional core (Sox2, Oct4 and Nanog), in addition to other factors (e.g. TGF-beta/Smad) that modulate transcriptional pathways related to the core regulation. Our algorithms also apply conservative rules during the search by assuming the hypothesis that these biding sites would be very conserved among mammals. This time we improved our search method applying Position Specific Scoring Matrixes (PSSM) in place of Regular Expressions (REs) in order to make our algorithms more sensitive, to decrease false positives rate (fpr), to be capable of detecting those genes regulated by TFBSs deviated from the consensus sequence represented by the REs, and to have a metric to compare TFBSs between orthologous genes.