TY  - JOUR
A1  - Thompson, William
A1  - Palumbo, Michael J.
A1  - Wasserman, Wyeth W.
A1  - Liu, Jun S.
A1  - Lawrence, Charles E.
T1  - Decoding Human Regulatory Circuits
Y1  - 2004/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1967 
EP  - 1974 
DO  - 10.1101/gr.2589004 
VL  - 14 
IS  - 10a 
UR  - http://genome.cshlp.org/content/14/10a/1967.abstract 
N2  - Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de novo, the cis features of these CRMs, their component TFBSs, and the properties of their spatial distribution. The algorithm finds 69% of experimentally reported TFBSs and 85% of the CRMs in a reference data set of regions upstream of genes differentially expressed in skeletal muscle cells. A discriminant procedure based on the output of the model specifically discriminated regulatory sequences in muscle-specific genes in an independent test set. Application of the method to the analysis of 2710 10-kb fragments upstream of annotated human genes identified 17 novel candidate modules with a false discovery rate ≤0.05, demonstrating the applicability of the method to genome-scale data. 
ER  -