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United States Department of Agriculture

Agricultural Research Service

Title: Effects of species combination on comparative analyses of conserved regulatory elements

item Liu, Ge - George
item Yang, Jianqi
item Matukumalli, Lakshmi
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Hanson, Richard

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/5/2007
Publication Date: 1/4/2008
Citation: Liu, G., Yang, J., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Hanson, R.W. 2008. Effects of species combination on comparative analyses of conserved regulatory elements. [abstract]. Pacific Symposium on Biocomputing. p.100.

Interpretive Summary:

Technical Abstract: Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprinting algorithm (TFLOC), was implemented and optimized to identify transcription factor binding sites (TFBSs) in mammalian promoter regions. To estimate the impact of evolutionary distance on predictive power, TFLOC and PhastCons were applied to various species combinations including human-chimpanzee-macaque, human-mouse-rat and human-cattle-dog. Computational prediction was compared with previously known sites at diverse genomic loci. Those newly discovered sites were further confirmed by experimental verifications including gel shifting and reporter assays. The best prediction was produced by the human-cattle-dog comparison with a higher sensitivity and a higher true-positive rate. The closer human-chimpanzee-macaque comparison produced more spurious sites, while the more distant human-mouse-rat comparison had a lower sensitivity. These results highlight the importance of choosing species at proper evolutionary distance for comparative genomics studies.

Last Modified: 09/25/2017
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