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dc.contributor.authorAndersen, Malin C.eng
dc.contributor.authorEngström, Pär G.eng
dc.contributor.authorLithwick, Stuarteng
dc.contributor.authorLithwick, Davideng
dc.contributor.authorEriksson, Pereng
dc.contributor.authorLenhard, Boriseng
dc.contributor.authorWasserman, Wyeth W.eng
dc.contributor.authorOdeberg, Jacobeng
dc.description.abstractIdentification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers). The RAVEN system is available at for all researchers interested in the detection and characterization of regulatory sequence variation.en_US
dc.rightsAttribution CC BYeng
dc.titleIn Silico Detection of Sequence Variations Modifying Transcriptional Regulationeng
dc.typeJournal articleeng
dc.typePeer reviewedeng
dc.rights.holderCopyright 2008 Andersen et al.
dc.source.journalPLoS Computational Biology
dc.subject.nsiVDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475nob

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