TY  - JOUR
A1  - King, David C.
A1  - Taylor, James
A1  - Zhang, Ying
A1  - Cheng, Yong
A1  - Lawson, Heather A.
A1  - Martin, Joel
A1  - ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis
A1  - Chiaromonte, Francesca
A1  - Miller, Webb
A1  - Hardison, Ross C.
T1  - Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
Y1  - 2007/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 775 
EP  - 786 
DO  - 10.1101/gr.5592107 
VL  - 17 
IS  - 6 
UR  - http://genome.cshlp.org/content/17/6/775.abstract 
N2  - Identification of functional genomic regions using interspecies comparison will be most effective when the full span of relationships between genomic function and evolutionary constraint are utilized. We find that sets of putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide span of evolutionary histories, ranging from stringent constraint shown by deep phylogenetic comparisons to recent selection on lineage-specific elements. This diversity of evolutionary histories can be captured, at least in part, by the suite of available comparative genomics tools, especially after correction for regional differences in the neutral substitution rate. Putative transcriptional regulatory regions show alignability in different clades, and the genes associated with them are enriched for distinct functions. Some of the putative regulatory regions show evidence for recent selection, including a primate-specific, distal promoter that may play a novel role in regulation. 
ER  -