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Open Access Highly Accessed Research article

2R and remodeling of vertebrate signal transduction engine

Lukasz Huminiecki12* and Carl Henrik Heldin1

Author Affiliations

1 Ludwig Institute for Cancer Research, Uppsala University, Box 595, SE-751 24 Uppsala, Sweden

2 Evolutionary Systems Biology, Department of Cell and Molecular Biology (CMB), Karolinska Institutet, P.O. Box 285, SE-171 77 Stockholm, Sweden

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BMC Biology 2010, 8:146  doi:10.1186/1741-7007-8-146

Published: 13 December 2010

Additional files

Additional file 1:

TableS1. 2ROs mapped to Entrez Genes.

Format: PDF Size: 323KB Download file

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Additional file 2:

TableS2_bp. 2RO overrepresented BP terms.

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Additional file 3:

TableS2_mf. 2RO overrepresented MF terms.

Format: PDF Size: 20KB Download file

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Additional file 4:

TableS2_cc. 2RO overrepresented CC terms.

Format: PDF Size: 16KB Download file

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Additional file 5:

TableS3_bp. 2RO underrepresented BP terms.

Format: PDF Size: 21KB Download file

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Additional file 6:

TableS3_mf. 2RO underrepresented MF terms.

Format: PDF Size: 19KB Download file

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Additional file 7:

TableS3_cc. 2RO underrepresented CC terms.

Format: PDF Size: 19KB Download file

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Additional file 8:

TableS3_not2R-over. Tandem/segmental duplication overrepresented BP terms.

Format: HTML Size: 7KB Download file

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Additional file 9:

TableS3_not2R-under. Tandem/segmental duplication underrepresented BP terms.

Format: HTML Size: 13KB Download file

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Additional file 10:

TableS4. 2RO overrepresented KEGG pathways.

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Additional file 11:

TableS5. 2RO overrepresented PFAM domains.

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Additional file 12:

TableS6. 349 2ROs preferentially expressed in brain.

Format: PDF Size: 65KB Download file

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Additional file 13:

TableS7_bp.html. 2ROs preferentially expressed in brain, overrepresented BP terms.

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Additional file 14:

TableS7_cc.html. 2ROs preferentially expressed in brain, overrepresented CC terms.

Format: HTML Size: 5KB Download file

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Additional file 15:

TableS7_mf.html. 2ROs preferentially expressed in brain, overrepresented MF terms.

Format: HTML Size: 8KB Download file

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Additional file 16:

FigureS1. Duplication timing and expression divergence (Kendall correlation).

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Additional file 17:

FigureS2. Duplication timing and expression divergence (Spearman's rank correlation).

Format: PDF Size: 47KB Download file

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Additional file 18:

FigureS3. Duplication timing and expression divergence (Manhattan distance).

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Additional file 19:

FigureS4. Duplication timing and expression (difference in breadth of expression).

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Additional file 20:

2ROs-bridged. Human 2RO bridged pairs.

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Additional file 21:

TableS8. 47 human tissues and cell lines in Gene Expression Atlas.

Format: PDF Size: 17KB Download file

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Additional file 22:

TableS9. Matrix of average PEM values across tissues and taxons.

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Additional file 23:

TableS10. Human genes with chromosomal location.

Format: PDF Size: 552KB Download file

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Additional file 24:

TableS11. Paralogy relationship between human 2ROs.

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Additional file 25:

TableS12. Fractions contained in 2RO-defined multiplicons by chromosome breakdown, paralog regions cover 83% of the human genome proving a WGD.

Format: PDF Size: 13KB Download file

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Additional file 26:

TableS13. Chromosomal clusters for gene duplications mapped to Chordata.

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Additional file 27:

TableS14. Chromosomal clusters for gene duplications mapped to Amniota/Tetrapoda.

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Additional file 28:

TableS15. Chromosomal clusters for duplications mapped to Mammalia/Eutheria/Theria.

Format: PDF Size: 14KB Download file

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Additional file 29:

TableS16. Chromosomal clusters for human-specific duplications.

Format: PDF Size: 14KB Download file

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