Open Access Software

CompMoby: Comparative MobyDick for detection of cis-regulatory motifs

Christina Chaivorapol1, Collin Melton23, Grace Wei34, Ru-Fang Yeh5, Miguel Ramalho-Santos346, Robert Blelloch23 and Hao Li1*

Author Affiliations

1 Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, Graduate Program in Biological and Medical Informatics; University of California, San Francisco, San Francisco, CA 94143-2540, USA

2 Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA

3 Institute for Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA

4 Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA

5 Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94107, USA

6 Departments of Obstetrics/Gynecology and Pathology, University of California, San Francisco, CA 94143, USA

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BMC Bioinformatics 2008, 9:455  doi:10.1186/1471-2105-9-455

Published: 27 October 2008

Additional files

Additional file 1:

Accession numbers of embryonic stem cells for upstream sequence analysis. Ensembl accession numbers of genes up-regulated in mouse embryonic stem cell compared with differentiated cells.

Format: XLS Size: 14KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Accession numbers of miR-1 over-expression. Ensembl accession numbers of genes down-regulated in human HeLa cells with miR-1 over-expression.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Accession numbers of miR-124 over-expression. Ensembl accession numbers of genes down-regulated in human HeLa cells with miR-124 over-expression.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Accession numbers of embryonic stem cells for 3' UTR analysis. Ensembl accession numbers of genes 1.5-fold up-regulated in all pair-wise comparisons of different types of mouse embryonic pluripotent cells to various types of differentiated cells.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Materials and methods for luciferase reporter assays. Materials and methods for ES cell culture and luciferase reporter assays in 3' UTR sequence analysis.

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data