Open Access Research article

Comparative modular analysis of gene expression in vertebrate organs

Barbara Piasecka123, Zoltán Kutalik23, Julien Roux13, Sven Bergmann23 and Marc Robinson-Rechavi13*

Author Affiliations

1 Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1005 Lausanne, Switzerland

2 Department of Medical Genetics, University of Lausanne, Rue de Bungon 27, CH-1015 Lausanne, Switzerland

3 Swiss Institute of Bioinformatics, Lausanne, Switzerland

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BMC Genomics 2012, 13:124  doi:10.1186/1471-2164-13-124

Published: 29 March 2012

Additional files

Additional file 1:

The list of co-modules obtained with the PPA run on data matched by orthologous genes. For every co-module we show number of genes, list of human and mouse organs assigned to the co-module, and the list of enriched GO categories for genes belonging to these co-modules.

Format: XLS Size: 75KB Download file

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Open Data

Additional file 2:

The list of co-modules obtained with the PPA run on data matched by homologous organs. For every co-module we show list of homologous organs, number of human and mouse genes assigned to the co-module, and the lists of enriched GO categories for human and mouse genes belonging to these co-modules.

Format: XLS Size: 109KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

The list of co-modules obtained with the PPA run on data matched by homologous organs. For every co-module we show the median dN/dS value for mouse and human genes separately. We also show a p-value of Wilcoxon signed rank test. In bold black wemarked modules with median dN/dS significantly lower than global median, and in bold red we marked co-modules with median dN/dS significantly higher than global median.

Format: XLS Size: 30KB Download file

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Additional file 4:

Analysis of the relationship between the co-modules and genes' age, duplicability, or essentiality.

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Additional file 5:

Expression conservation rate (γ) for other system-specific co-modules. The median γ for all co-modules is marked with dotted line. Abbreviations for organ names: ag - adrenal gland; am - amygdala; bm - bone marrow; ce - cerebellum; cc - cerebral cortex; drg - dorsal root ganglion; he - heart; hp - hypophysis; ht - hypothalamus; li - liver; lu - lung; ln - lymph node; ki - kidney; ob - olfactory bulb; ov - ovary; pl - placenta; pr - prostate; sc - spinal cord; te - testis; tm - thymus; to -tongue; tra - trachea; ut - uterus.

Format: PDF Size: 23KB Download file

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Additional file 6:

The list of co-modules obtained with the PPA run on data matched by homologous organs. For every co-module we show list of homologous organs assigned to the co-module and the list of the zebrafish organs enriched in expression of genes orthologous to mouse genes assigned to the co-module.

Format: XLS Size: 52KB Download file

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Additional file 7:

The list of homologous organ groups and their corresponding sample names in human and mouse expression data sets.

Format: XLS Size: 40KB Download file

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