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Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2

Stephan Struckmann12*, Daniel Esch3, Hans Schöler34 and Georg Fuellen1*

Author Affiliations

1 University of Rostock, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Heydemannstrasse 8, 18057 Rostock, Germany

2 E.M.A. University of Greifswald, Institute for Mathematics and Computer Science, Rathenaustrasse 47, 17487 Greifswald, Germany

3 Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany

4 Medical Faculty, University of Münster, Domagkstrasse 3, 48149 Münster, Germany

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BMC Evolutionary Biology 2011, 11:267  doi:10.1186/1471-2148-11-267

Published: 24 September 2011

Additional files

Additional file 1:

Supplementary methods and results. The pattern search algorithm is described. Furthermore, all additional output files that are not described in the main article are listed here.

Format: PDF Size: 10.3MB Download file

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Additional file 2:

BED detail format file with the annotations for the CR3 region. This file can be uploaded to UCSC. It contains the transcription factor binding site pattern found in the conserved murine CR3 region near the Pou5f1 gene. All transcription factor binding sites are annotated with their STRING [31,32] and their iHOP [33,34] annotations, if available.

Format: TXT Size: 161KB Download file

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Additional file 3:

BED detail format file with the annotations for the CR1 region. This file can be uploaded to UCSC. It contains all transcription factor binding site patterns found in the conserved murine CR1 region near the Pou5f1 gene. All transcription factor binding sites are annotated with their STRING [31,32] and their iHOP [33,34] annotations, if available.

Format: TXT Size: 1.2MB Download file

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Additional file 4:

BED detail format file with the annotations for the SRR1 region. This file can be uploaded to UCSC. It contains all transcription factor binding site patterns found in the conserved murine SRR1 region near the Sox2 gene. All transcription factor binding sites are annotated with their STRING [31,32] and their iHOP [33,34] annotations, if available.

Format: TXT Size: 361KB Download file

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Additional file 5:

BED detail format file with the annotations for the N1 region. This file can be uploaded to UCSC. It contains all transcription factor binding site patterns found in the conserved murine N1 region near the Sox2 gene. All transcription factor binding sites are annotated with their STRING [31,32] and their iHOP [33,34] annotations, if available.

Format: TXT Size: 1.2MB Download file

Open Data

Additional file 6:

CR1 patterns, Homology-based figure. The patterns and the transcription factor binding sites found in the murine CR1 region. See Figure 7 for further explanations.

Format: PDF Size: 1.6MB Download file

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Additional file 7:

SRR1 patterns, Homology-based figure. The patterns and the transcription factor binding sites found in the murine SRR1 region. See Figure 7 for further explanations.

Format: PDF Size: 2MB Download file

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Open Data

Additional file 8:

N1 patterns, Homology-based figure. The patterns and the transcription factor binding sites found in the murine N1 region. See Figure 7 for further explanations.

Format: PDF Size: 2.4MB Download file

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Additional file 9:

CR3 pattern, table format. The pattern found in the murine CR3 region. See also Additional File 3 for a more detailed version of this table.

Format: XLS Size: 29KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

CR3 pattern, detailed table format. The pattern found in the murine CR3 region, detailed version of Additional File 2.

Format: XLS Size: 68KB Download file

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Additional file 11:

CR1 patterns, table format. The patterns found in the murine CR1 region. See also Additional File 7 for a more detailed version of this table.

Format: XLS Size: 269KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 12:

CR1 patterns, detailed table format. The patterns found in the murine CR1 region, detailed version of Additional File 6.

Format: XLS Size: 589KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 13:

SRR1 patterns, table format. The patterns found in the murine SRR1 region. See also Additional File 11 for a more detailed version of this table.

Format: XLS Size: 306KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 14:

SRR1 patterns, detailed table format. The patterns found in the murine SRR1 region, detailed version of Additional File 10.

Format: XLS Size: 548KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 15:

N1 patterns, table format. The patterns found in the murine N1 region. See also Additional File 15 for a more detailed version of this table.

Format: XLS Size: 795KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 16:

N1 patterns, detailed table format. The patterns found in the murine N1 region, detailed version of Additional File 14.

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 17:

CR3 pattern, Alignment based figure. The pattern and the transcription factor binding sites found in the murine CR3 region. In principle, the elements of this figure correspond to those in Figure 7. Obviously, the alignment-based figures are much larger than their homology-based version. In contrast to the homology-based figure type, the leaves of the species tree on the left are corresponding to the sequences of the extant species on the right. The sequences are shown in a sequence alignment and the transcription factor binding site predictions are plotted below the sequences. Because the species belonging to each prediction is obviously determined by its vertical position (the leaves are not color coded here), only the thicker part of the colored overlays (see Figure 7) is informative and thus it is shown; it denotes the pattern by referring to its color. To keep the figures readable, by default only the first 10 patterns (ordered by branch length score) are shown in the alignment-based figures.

Format: PDF Size: 1.6MB Download file

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Additional file 18:

CR1 patterns, Alignment based figure. The patterns and the transcription factor binding sites found in the murine CR1 region. See Additional File 17 for an explanation.

Format: PDF Size: 8.1MB Download file

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Additional file 19:

SRR1 patterns, Alignment based figure. The patterns and the transcription factor binding sites found in the murine SRR1 region. See Additional File 17 for an explanation.

Format: PDF Size: 10.9MB Download file

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Additional file 20:

N1 patterns, Alignment based figure. The patterns and the transcription factor binding sites found in the murine N1 region. See Additional File 17 for an explanation.

Format: PDF Size: 11MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data