INSECT: In silico search for co-occurring transcription factors

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

Rosario

Congreso; 4to. Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) y 4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SolBio); 2013

Background Regulation of transcription occurs through the concerted actions of multiple transcription factors (TFs) that bind cooperatively to cis-regulatory modules (CRMs) of genes. These CRMs usually contain a variable number of transcription factor-binding sites (TFBSs) involved in related cellular and physiological processes. Although several attempts were previously reported to predict the potential binding of TFs at TFBSs within CRMs, these have been only partially successful due to the excessive background that usually emerges as a consequence of the experimental conditions. It would be helpful to have confident, updated and user-friendly tools that assist for the identification of TFBSs and CRMs for gene(s) of interest. Materials and methods Genes and putative regulatory regions from the genomes of fourteen organisms can be defined and retrieved from Ensembl. Additionally, a multi-fasta file with up to 500 sequences can be uploaded. In order to reduce the false positive rate, INSECT gives to option to apply a phylogenetic footprinting search analyzing the conservation with orthologous genes or sequences. Position weight matrices (PWMs) representing TFBSs from JASPAR, TRANSFAC and UniPROBE databases can be selected for the search, or users can build their own PWMs from a set of aligned target sequences or upload their own PWMs. INSECT offers two search types with the possibility to include different search restrictions. INSECT provides Gene ontology mapping, diagrams with the detected TFBSs and CRMs along with the gene exons/introns structure, spreadsheets with the TFBSs sequences and PWM scores, and GFF files that can be automatically submitted and opened into the UCSC Genome Browser [http://genome.ucsc.edu/]. Results Here we present INSECT (IN-silico SEarch for Co-occurring Transcription factors) a novel web server for searching potential TFBSs and CRMs. By combining different strategies, INSECT allows for complete and flexible analysis of multiple co-occurring TFs binding sites. INSECT was tested by searching two experimental datasets for TFBSs of Sox2 and Oct-4, two transcription factors involved in maintaining pluripotency in embryonic stem cells. We compared INSECT results and performance with other existing motif search tools. We show that INSECT outperformed the other tools in almost every analysis. Additionally we have included several modules within INSECT implementation that help researchers to perform further analysis on the search results improving the filtering of false positives and assisting in the construction of new hypothesis. Conclusions INSECT is a powerful tool for search and analyze potential CRM presence on large gene datasets, in a fully web server with a user-friendly interface and with the integration of several methods that aim to assist during results visualization and analysis.