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Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

Tanya Vavouri12*, Klaudia Walter3, Walter R Gilks4, Ben Lehner5 and Greg Elgar2

Author Affiliations

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

2 School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK

3 MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, UK

4 Department of Statistics, University of Leeds, Leeds LS2 9JT, UK

5 EMBL/CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), UPF, C/Dr. Aiguader 88, Barcelona 08003, Spain

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Genome Biology 2007, 8:R15  doi:10.1186/gb-2007-8-2-r15

Published: 2 February 2007

Additional files

Additional data file 1:

Distribution of wCNEs along each chromosome.

Format: PDF Size: 136KB Download file

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Open Data

Additional data file 2:

Distribution of distances between CNEs in both the C. elegans and the H. sapiens genomes and for randomized CNE locations.

Format: PDF Size: 20KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional data file 3:

Distribution of distances between intergenic wCNEs and their nearest genes.

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Open Data

Additional data file 4:

Top-level InterPro protein domains significantly enriched in CNE-associated genes compared to the rest of the genes in the (a) H. sapiens and (b) C. elegans genomes.

Format: PDF Size: 113KB Download file

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Open Data

Additional data file 5:

Enrichment for transcription factors among wCNE-associated genes, using two different collections of predicted transcription factors from the C. elegans genome.

Format: PDF Size: 15KB Download file

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Open Data

Additional data file 6:

wCNEs overlapping known cis-regulatory elements.

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Additional data file 7:

Annotation features from WormBase that were used to annotate wCNEs.

Format: PDF Size: 58KB Download file

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Open Data

Additional data file 8:

Sequences of the 2,084 wCNEs.

Format: TXT Size: 185KB Download file

Open Data

Additional data file 9:

Coordinates of the wCNEs in the C. elegans genome, their nearest genes and their human orthologs.

Format: XLS Size: 197KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 10:

Coordinates of the human CNEs from Woolfe et al. [4] with their nearest genes assigned using the same method as for the wCNEs.

Format: XLS Size: 104KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data