Detection of functional DNA motifs via statistical over-representation.

By Martin C. Frith, Yutao Fu, Liqun Yu, Jiang-fan Chen, Ulla Hansen, Zhiping Weng. Nucleic Acids Research, 2004

466 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4dd11fe2f71a03dfe98d1c2f27fe0ea474960e37

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Citations in the corpus

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers (2010, methodology): “Then we divided the enhancers in three groups based on Pol_II behavior (constitutive, inducible, and repressed) and used a statistical approach [69] to score TFBS enrichment in each group relative to two background sets (namely the whole mouse chr 19 and a set of all 5 kb sequences located upstream ”
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes (2005, background): “Other resources are available for detecting and visualizing binding sites within the conserved regions of human genes [Consite (11), rVISTA (38), dbTSS (39), CONREAL (40), CORG (41)], as well as for identifying statistically over-represented motifs in the promoters of related sequences [Clover (42),”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, unknown): “Successful RACE reactions (%) Index TF 5' RACE 3' RACE 5' and 3' RACE 5' or 3' RACE Transcription on both strands No transcript detected Exonic 20 19 (95) 19 (95) 16 (80) 20 (100) 19 (95) 0 (0) Intronic 90 71 (79) 77 (86) 66 (73) 79 (88) 65 (72) 11 (12) Intergenic 90 62 (69) 65 (72) 44 (49) 77 (86) ”
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections (2014, methodology): “Although a lot of progress has been made over the last decade and many motif discovery methods have been developed and refined (reviewed in [16–19]), motif discovery methods alone are not sufficient to map a gene regulatory network, nor can they be applied to noisy gene sets containing mixtures of…”
High-resolution mapping and characterization of open chromatin across the genome. (2008, methodology): “…University, Boston, MA 02215, USA 3Center for Cancer Research, National Cancer Institute 4National Human Genome Research Institute National Institutes of Health, Bethesda, MD 20892, USA *Correspondence: terry.furey@duke.edu (T.S.F.), greg.crawford@duke.edu (G.E.C.) DOI 10.1016/j.cell.2007.12.014”