Gene set enrichment analysis for non-monotone association and multiple experimental categories

doi:10.1186/1471-2105-9-481

BMC Bioinformatics

Volume 9

Viewing options:

Abstract
Full text
PDF (373KB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Lin R
Dai S
Irwin RD
Heinloth AN
Boorman GA
Li L

on PubMed

Lin R
Dai S
Irwin RD
Heinloth AN
Boorman GA
Li L
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Methodology article

Gene set enrichment analysis for non-monotone association and multiple experimental categories

Rongheng Lin¹ , Shuangshuang Dai² , Richard D Irwin³ , Alexandra N Heinloth⁴ , Gary A Boorman⁵ and Leping Li¹

¹Biostatistics Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA

²Alpha-Gamma Technologies, Inc., Raleigh NC 27609, USA

³Environmental Toxicology Program, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA

⁴Laboratory of Molecular Toxicology, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA

⁵Covance Inc., Vienna, VA 22066, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:481doi:10.1186/1471-2105-9-481


Published:	14 November 2008

Additional files

Additional file 1:

Supplement: Gene Set Enrichment Analysis for non-monotone association and multiple experimental categories. The file includes three sections: 1, the exploration on distribution of R²under permutation; 2, gene set data preparation; 3. identified gene sets and biological interpretation.

Format: PDF Size: 168KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

Sets and Expression. The intermediate analysis results of NCT compendium data set. Sets directory contains lists of identified gene sets under different across-compound (category) selection criteria. Compound specific p-values, set size, etc are provided. Expression directory contains extracted expression data for respective identified gene sets.

Format: ZIP Size: 3.5MB Download file

Additional file 3:

Heat maps of sets in A_LB(0:1). Heat maps of gene sets in A_LB(0:1). Both liver and blood data are presented for each identified set. Alt level is included after log10 transformation.

Format: PPT Size: 860KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Additional file 4:

Associations between genes in the identified set glycolysis and gluconeogenesis for liver data. Figures that show associations between genes in the identified set glycolysis and gluconeogenesis for liver data. All 8 compounds are presented, including monocrotaline (Figure 3 in the article).

Format: PDF Size: 225KB Download file

This file can be viewed with: Adobe Acrobat Reader