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• W2156885385 abstract "Metazoan transcription regulation occurs through the concerted action of multiple transcription factors that bind co-operatively to cis-regulatory modules (CRMs). The annotation of these key regulators of transcription is lagging far behind the annotation of the transcriptome itself. Here, we give an overview of existing computational methods to detect these CRMs in metazoan genomes. We subdivide these methods into three classes: CRM scanners screen sequences for CRMs based on predefined models that often consist of multiple position weight matrices (PWMs). CRM builders construct models of similar CRMs controlling a set of co-regulated or co-expressed genes. CRM genome screeners screen sequences or complete genomes for CRMs as homotypic or heterotypic clusters of binding sites for any combination of transcription factors. We believe that CRM scanners are currently the most advanced methods, although their applicability is limited. Finally, we argue that CRM builders that make use of PWM libraries will benefit greatly from future advances and will prove to be most instrumental for the annotation of regulatory regions in metazoan genomes." @default.
• W2156885385 created "2016-06-24" @default.
• W2156885385 creator A5065115714 @default.
• W2156885385 creator A5079808888 @default.
• W2156885385 date "2009-06-04" @default.
• W2156885385 modified "2023-09-27" @default.
• W2156885385 title "Computational methods for the detection of cis-regulatory modules" @default.
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• W2156885385 doi "https://doi.org/10.1093/bib/bbp025" @default.
• W2156885385 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19498042" @default.
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