Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

doi:10.1186/1471-2105-5-129

BMC Bioinformatics
Volume 5

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Gaul U
Siggia ED

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Research article

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

Saurabh Sinha¹ , Mark D Schroeder² , Ulrich Unnerstall² , Ulrike Gaul² and Eric D Siggia¹

¹Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Ave, New York, NY10021, USA

²Laboratory of Developmental Neurogenetics, The Rockefeller University, 1230 York Ave, New York, NY10021, USA

author email corresponding author email

BMC Bioinformatics 2004, 5:129doi:10.1186/1471-2105-5-129


Published:	9 September 2004

Additional 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, 2^ndorder 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, 1^storder 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