Email updates

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

Open Access Highly Accessed Research article

An integrative approach to inferring biologically meaningful gene modules

Ji-Hoon Cho, Kai Wang and David J Galas*

Author Affiliations

Institute for Systems Biology, 401 N Terry Avenue, Seattle, WA 98109, USA

For all author emails, please log on.

BMC Systems Biology 2011, 5:117  doi:10.1186/1752-0509-5-117

Published: 26 July 2011

Additional files

Additional file 1:

Additional enrichment results. The number of enriched modules, number of annotation terms and F-measures (GO, GO BP and MIPS FunCat) were shown as functions of p-value. Results for MATISSE and ICMg were obtained using the mean and standard deviation values of 20 runs.

Format: PDF Size: 44KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Coherency and depth of significantly enriched GO BP terms. Average expression coherency and depth of significantly enriched GO BP terms in the modules identified by different methods were calculated as described in the method section. Large coherency and depth values mean that GO BP terms enriched in the same module are semantically similar and associated with specific functions, respectively. For MATISSE and ICMg, mean and standard deviation over 20 runs were taken.

Format: PDF Size: 87KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Summary of the modules identified by three different methods. The assignments of 1990 genes in MATISSE data into 24 modules identified by SSIM, MATISSE and ICMg were summarized in Table S1 (see methods). GO BP enrichment results of the modules obtained from SSIM, MATISSE and ICMg were also shown in Table S2, S3 and S4, respectively.

Format: XLS Size: 252KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Results of SSIM method over a wide range of preference values. The number of modules and average expression, topological and semantic similarities of the modules were expressed as functions of preference.

Format: PDF Size: 93KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

An example of the extension of a module

Format: PDF Size: 220KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

An application of SSIM to prion network datasets

Format: PDF Size: 1.4MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data