Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder Export

@article{citeulike:5779057, abstract = {We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. 10.1093/dnares/dsp014}, author = {Sharov, Alexei A. and Ko, Minoru S. H.}, booktitle = {DNA Res}, citeulike-article-id = {5779057}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/dnares/dsp014}, citeulike-linkout-1 = {http://dnaresearch.oxfordjournals.org/content/dsp014v1/.abstract}, citeulike-linkout-2 = {http://dnaresearch.oxfordjournals.org/content/dsp014v1/.full.pdf}, citeulike-linkout-3 = {http://dnaresearch.oxfordjournals.org/cgi/content/abstract/16/5/261}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19740934}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19740934}, day = {1}, doi = {10.1093/dnares/dsp014}, issn = {1756-1663}, journal = {DNA Res}, keywords = {binding, binding-motif, binding-site, consensus, ctcf, k-word, motif, tf, transcription-factor, word}, month = {October}, number = {5}, pages = {261--273}, posted-at = {2009-10-28 22:59:36}, priority = {5}, title = {Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder}, url = {http://dx.doi.org/10.1093/dnares/dsp014}, volume = {16}, year = {2009} }

TY - JOUR ID - citeulike:5779057 L3 - citeulike-article-id:5779057 N2 - We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. 10.1093/dnares/dsp014 IS - 5 JF - DNA Res SN - 1756-1663 EP - 273 TI - Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder VL - 16 T2 - DNA Res SP - 261 KW - binding KW - binding-motif KW - binding-site KW - consensus KW - ctcf KW - k-word KW - motif KW - tf KW - transcription-factor KW - word AU - Sharov, Alexei AU - Ko, Minoru PY - 2009/10/01/ UR - http://dx.doi.org/10.1093/dnares/dsp014 ER -