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Open Access Highly Accessed Methodology article

Eigengene networks for studying the relationships between co-expression modules

Peter Langfelder1 and Steve Horvath2*

Author Affiliations

1 Department of Human Genetics, University of California, Los Angeles, CA 90095, USA

2 Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA

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BMC Systems Biology 2007, 1:54  doi:10.1186/1752-0509-1-54

Published: 21 November 2007

Additional files

Additional file 1:

Detailed description of data for Application 1, differential eigengene analysis of human and chimpanzee brain expression data. This document describes the human and chimp microarray data sets and the module detection method. The R code posted on our web page allows one to reproduce the Figures and tables reported in the main text.

Format: DOC Size: 49KB Download file

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Open Data

Additional file 2:

Comparing human-chimp consensus modules to their human data set specific counterparts. This document describes a comparison between our human-chimp consensus modules and the human-specific modules detected by Oldham et al [11].

Format: PDF Size: 47KB Download file

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Open Data

Additional file 3:

Detailed description of data for Application 2, differential eigengene network analysis of expression data from four tissues in female mice. This document describes the mouse tissue microarray data sets and the module detection method. The R code posted on our web page allows one to reproduce the Figures and tables reported in the main text.

Format: DOC Size: 49KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Functional enrichment analysis of consensus modules across four tissues of female mice. In this document we report functional enrichment p-values provided by the online tool DAVID [20]. The results show that our consensus modules are highly significantly enriched with known gene ontologies.

Format: PDF Size: 84KB Download file

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Additional file 5:

Detailed description of data for Application 3, differential eigengene network analysis between female and male mice. In this document we describe the details of female and male mouse liver data and the differential eigengene network analysis. We analyze the relationship between consensus modules and clinical traits. The R code posted on our web page allows one to reproduce the Figures and tables reported in the main text.

Format: DOC Size: 45KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

Comparing female-male mouse liver consensus modules to their female data set specific counterparts. This document describes a comparison between our male-female mouse consensus modules and the female liver-specific modules detected by Ghazalpour et al [18].

Format: PDF Size: 47KB Download file

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Open Data

Additional file 7:

Simulation of gene expression data sets. This document describes the simulation of gene expression data sets with a modular structure. The simulation R code can be found on our web page.

Format: PDF Size: 72KB Download file

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Open Data