Prediction of regulatory elements
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Prediction of regulatory elements. / Sandelin, Albin.
In: Methods in Molecular Biology, Vol. 453, 2008, p. 233-44.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Prediction of regulatory elements
AU - Sandelin, Albin
N1 - Keywords: Animals; Binding Sites; Computational Biology; Humans; Promoter Regions (Genetics); Regulatory Elements, Transcriptional; Transcription Factors
PY - 2008
Y1 - 2008
N2 - Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene. As wet-lab methods are time consuming and expensive, it is not realistic to identify TFBS for all uncharacterized genes in the genome by purely experimental means. Computational methods aimed at predicting potential regulatory regions can increase the efficiency of wet-lab experiments significantly. Here, methods for building quantitative models describing the binding preferences of transcription factors based on literature-derived data are presented, as well as a general protocol for scanning promoters using cross-species comparison as a filter (phylogenetic footprinting).
AB - Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene. As wet-lab methods are time consuming and expensive, it is not realistic to identify TFBS for all uncharacterized genes in the genome by purely experimental means. Computational methods aimed at predicting potential regulatory regions can increase the efficiency of wet-lab experiments significantly. Here, methods for building quantitative models describing the binding preferences of transcription factors based on literature-derived data are presented, as well as a general protocol for scanning promoters using cross-species comparison as a filter (phylogenetic footprinting).
U2 - 10.1007/978-1-60327-429-6_11
DO - 10.1007/978-1-60327-429-6_11
M3 - Journal article
C2 - 18712306
VL - 453
SP - 233
EP - 244
JO - Methods in Molecular Biology
JF - Methods in Molecular Biology
SN - 1064-3745
ER -
ID: 9068098