منابع مشابه
Computational detection of cis-regulatory modules
MOTIVATION The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription. RESULTS Based on the hypothesis that genes that are needed in exactly th...
متن کاملAn Integrated Predictor for Cis-Regulatory Modules
Various cis-regulatory module (CRM) predictors have been proposed in the last decade. Several well-established CRM predictors adopted different categories of prediction strategies, including window clustering, probabilistic modeling and phylogenetic footprinting. Appropriate integration of them has a potential to achieve high quality CRM prediction. This study analyzed four existing CRM predict...
متن کاملDiscovering cis-regulatory modules by optimizing barbecues
Gene expression in eukaryotic cells is regulated by a complex network of interactions, in which transcription factors and their binding sites on the genomic DNA play a determining role. As transcriptions factor rarely, if ever, act in isolation, binding sites of interacting factors are typically arranged in close proximity forming so-called cis-regulatory modules. Even when the individual bindi...
متن کاملTwine: display and analysis of cis-regulatory modules
UNLABELLED Many algorithms analyze enhancers for overrepresentation of known and novel motifs, with the goal of identifying binding sites for direct regulators of gene expression. Twine is a Java GUI with multiple graphical representations ('Views') of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of phylogenetic conservati...
متن کاملLmx1b-targeted cis-regulatory modules involved in limb dorsalization.
Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct gene targets in the limb have been confirmed. To determine direct targets, we performed a chromatin immunoprecipitation against Lmx1b in mouse limbs at embryonic day 12.5 followed by next-generation seq...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2002
ISSN: 1465-6906
DOI: 10.1186/gb-spotlight-20020123-01