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Resource: PRISM offers a comprehensive genomic approach to transcription factor function prediction
- Aaron M. Wenger,
- Shoa L. Clarke,
- Harendra Guturu,
- Jenny Chen,
- Bruce T. Schaar,
- Cory Y. McLean,
- and Gill Bejerano
Genome Res. May 2013 23: 889-904; Published in Advance February 4, 2013, doi:10.1101/gr.139071.112
...functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach...
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LETTER: Serum response factor binding sites differ in three human cell types
- Sara J. Cooper,
- Nathan D. Trinklein,
- Loan Nguyen,
- and Richard M. Myers
Genome Res. February 2007 17: 136-144; Published in Advance January 2, 2007, doi:10.1101/gr.5875007
...al. 2006 ). Another SRF-regulated gene, heart alpha-kinase 2 ( ALPK2 ), is expressed in heart, skeletal muscle, and cardiomyocytes ( Jongeneel et al. 2005 ). ALPK2 is one member of a protein kinase-like family whose other members phosphorylate myosin heavy chains. We also discovered a binding site...

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