Research article
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
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* Corresponding author: Saurabh Sinha saurabh@lonnrot.rockefeller.edu
1 Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, New York, NY10021, USA
2 Laboratory of Developmental Neurogenetics, The Rockefeller University, 1230 York Ave, New York, NY10021, USA
BMC Bioinformatics 2004, 5:129 doi:10.1186/1471-2105-5-129
Published: 9 September 2004Additional files
Additional File 1:
Test Genes List of 2167 genes with expression information. (Source BDGP + literature.)
Format: TXT Size: 31KB Download file
Additional File 2:
Patterned Genes List of 286 genes with blastoderm pattern, as determined by manual inspection of in-situ expression pattern. (Source BDGP + literature.)
Format: TXT Size: 8KB Download file
Additional File 3:
Additional Genes List of 2065 genes that are ubiquitous, maternal only, or not expressed. (Source BDGP.)
Format: TXT Size: 15KB Download file
Additional File 4:
Predicted CRM's – two species List of predicted CRM's using two-species Stubb with a global, 2nd order background, sorted in decreasing order of Stubb score.
Format: HTML Size: 4.2MB Download file
Additional File 5:
Predicted CRM's – single species List of predicted CRM's using single-species Stubb with a local, 1st order background, sorted in decreasing order of Stubb score. This list of predictions, as well as that in Additional File 4 (above), is meant to be as inclusive as possible; therefore, the specificity of the lowest ranked predictions may be poor.
Format: HTML Size: 2.3MB Download file