Open Access Research article

Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers

Hugo J Parker1, Paul Piccinelli1, Tatjana Sauka-Spengler2, Marianne Bronner3 and Greg Elgar1*

Author Affiliations

1 Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK

2 Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK

3 Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA

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BMC Genomics 2011, 12:637  doi:10.1186/1471-2164-12-637

Published: 30 December 2011

Additional files

Additional file 1:

Genomic sequences used to generate MLAGAN alignment. The genomic sequences of human, fugu, zebrafish and lamprey used to generate the MLAGAN alignment in this study.

Format: TXT Size: 86KB Download file

Open Data

Additional file 2:

CNEs functionally tested for this study. The sequences of the CNEs of zebrafish (dr) and lamprey (pm) that were tested by reporter assay in zebrafish embryos for this study.

Format: TXT Size: 9KB Download file

Open Data

Additional file 3:

The frequency of Pbx-Hox motifs in different test sets. A table describing the frequency of Pbx-Hox motifs in different test sets, compared with 1000 randomised controls.

Format: DOC Size: 37KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

The frequency of KR motifs in different control sets. A table listing the frequency of KR motifs, compared to shuffled versions, in different control sets.

Format: DOC Size: 46KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

The frequency of Meis motifs in Human CNEs. A table listing the frequency of Meis motifs, compared to shuffled versions in human CONDOR CNEs.

Format: DOC Size: 55KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

The frequency of KR motifs in CNEs at different gene loci. A table listing the frequency of KR motifs in CNEs at different gene loci.

Format: DOC Size: 134KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 7:

The CONDOR CNE set. 6693 non-redundant human CNE sequences, shared between human and fugu, retrieved from the CONDOR database.

Format: TXT Size: 889KB Download file

Open Data

Additional file 8:

Lamprey CNEs. Lamprey sequences of 246 CNEs shared between jawed vertebrates and lamprey (from the lamprey CNE alignment set).

Format: TXT Size: 33KB Download file

Open Data

Additional file 9:

Zebrafish CNEs. Zebrafish sequences of 4259 CNEs shared between human, fugu and zebrafish (from the gnathostome CNE alignment set).

Format: TXT Size: 588KB Download file

Open Data

Additional file 10:

CNEs from the VISTA Enhancer Browser. 1307 human sequences from the VISTA Enhancer Browser http://enhancer.lbl.gov/ webcite.

Format: TXT Size: 2.1MB Download file

Open Data

Additional file 11:

CNEs from the cneBrowser. 146 functionally tested zebrafish sequences from the cneBrowser http://bioinformatics.bc.edu/chuanglab/cneBrowser/#home webcite.

Format: TXT Size: 64KB Download file

Open Data

Additional file 12:

TGATNNAT motif hits on the human CONDOR CNEs. Hits of the TGATNNAT motif on the human CONDOR CNEs listed by CNE with details of the start and finish of the motif within the CNE.

Format: TXT Size: 45KB Download file

Open Data

Additional file 13:

TGATNNATKR motif hits on the human CONDOR CNEs. Hits of the TGATNNATKR motif on the human CONDOR CNEs listed by CNE with details of the start and finish of the motif within the CNE.

Format: TXT Size: 18KB Download file

Open Data