Wednesday, March 13, 2013

Fwd: LASAGNA: A better taste for transcription factor analysis

Fwd: please follow footer link

Transcription factors (TF) play a critical role in cell homeostasis, signaling, and response to stimuli by binding gene regulatory regions in a sequence-specific manner and subsequently alterating gene expression. Functional studies of individual TFs can provide specific details on the interactions between a TF and its binding site (TFBS), but such functional analyses are specific, expensive, and time-consuming. As an alternative, researchers frequently take advantage of computational tools to scan genomic sequences and make predictions regarding putative TFBSs. In addition to basic TF search functions, these currently available tools can also search variable length binding sites, retrieve promoter sequences, and predict binding specificities, among other functions. Although several useful programs are currently available to facilitate such computational studies of TFBS, none of these can complete all the possible analysis steps just described, requiring interested users to go between several programs for their searches. To improve the efficiency of TF analysis, Chih Lee and Chun-His Huang at the University of Connecticut describe the development of a web-based program they call LASAGNA-Search in the current issue of BioTechniques. LASAGNA-Search allows for complete TFBS search and visualization, including the ability to search variable-length TFBS, incorporation of five pre-computed models and 1726 TF models collected from user-curated TF databases, use of position dependence data for modeling, automatic promoter sequence retrieval, visualization of search results in the UCSC Genome Browser, and construction of gene regulatory networks, all without leaving the webpage. LASAGNA-Search currently supports promoter searches for seven species, and the authors extensively compared and contrasted their new pipeline with other available programs, demonstrating that LASAGNA-Search consistently outperforms MAPPER2, the most closely related program. LASAGNA-Search promises a more efficient and streamlined method for TFBS searches, with the added promise of expanded content and improved features in the future."

(Via doi 10.2144/000113999.)