title: INSECT: IN-silico SEarch for Co-occurring Transcription factors.
abstract: BACKGROUND
  Transcriptional regulation 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. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been effective in detecting TFBSs and nucleosome location to identify potential CRMs in genome-wide studies. Although several attempts were previously reported to predict the potential binding of TFs at TFBSs within CRMs by comparing different ChIP-seq data, these have been hampered by excessive background, usually emerging as a consequence of experimental conditions. To understand these complex regulatory circuits, it would be helpful to have reliable and updated user-friendly tools to assist in the identification of TFBSs and CRMs for gene(s) of interest.
  
  
  RESULTS
  Here we present INSECT (IN-silico SEarch for Co-occurring Transcription factors), a novel web server for identifying potential TFBSs and CRMs in gene sequences. By combining several strategies, INSECT provides flexible analysis of multiple co-occurring TFBSs, by applying differing search schemes and restriction parameters. availability and implementation: INSECT is freely available as a web server at http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT .
authors.affiliation: Instituto de Ecología, Genética y Evolución (IEGEBA)-CONICET, Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, C1428EGA, Buenos Aires, Argentina and Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) -CONICET- Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina.
authors.forename: Cristian O
authors.initials: CO
authors.lastname: Rohr
authors.forename: R Gonzalo
authors.initials: RG
authors.lastname: Parra
authors.forename: Patricio
authors.initials: P
authors.lastname: Yankilevich
authors.forename: Carolina
authors.initials: C
authors.lastname: Perez-Castro
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D003198:Computer Simulation; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors