Email updates

Keep up to date with the latest news and content from BMC Systems Biology and BioMed Central.

Open Access Highly Accessed Methodology article

Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease

Michael C Oldham1*, Peter Langfelder2 and Steve Horvath23*

Author Affiliations

1 Department of Neurology, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, USA

2 Department of Human Genetics, University of California, Los Angeles, USA

3 Department of Biostatistics, University of California, Los Angeles, CA, USA

For all author emails, please log on.

BMC Systems Biology 2012, 6:63  doi:10.1186/1752-0509-6-63

Published: 12 June 2012

Additional files

Additional file 1:

Supplementary information. PDF file containing Supplementary Methods, Supplementary References, and Supplementary Figures (1–8).

Format: PDF Size: 12.9MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Sample information. XLS table that summarizes sample information, including Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/ webcite) sample ID, sample labels, diagnosis, severity grade, age, sex, individual ID, hybridization date, hybridization batch assignment, and country of processing, as described in ref. [14].

Format: XLS Size: 69KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

SampleNetwork R tutorial. DOC file containing annotated R code and detailed instructions for executing the SampleNetwork and ModuleSampleNetwork R functions. The datasets that are referenced in the tutorial and analyzed in this study can be downloaded from: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/SampleNetwork webcite.

Format: DOC Size: 13.7MB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Summary of differential expression, functional enrichment, and module membership for genes in the salmon module. XLS table that summarizes the extent of differential expression, functional enrichment, and membership strength for the salmon module. Differential expression analyses include CTRL vs. HD human caudate nucleus samples [14], CTRL vs. HD human laser-microdissected striatal neurons [14], and wild-type mice vs. a mutant mouse model of HD cultured primary striatal neurons [20]. Functional enrichment categories included G-protein coupled receptors, phosphatidylinositol signaling, calmodulin binding, ion transport, and calcium ion binding; all of these categories were significantly enriched in the salmon module [21]. Module membership values and corresponding P-values are taken from ref. [21].

Format: XLS Size: 80KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Ingenuity Pathways Analysis of salmon module genes. XLS table that reports false-discovery rate (FDR)-corrected P-values for the 500 most enriched functionally annotated categories of genes in the salmon module from Ingenuity Pathways Analysis (IPA; http://www.ingenuity.com/ webcite).

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data