Email updates

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

Open Access Highly Accessed Research article

GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network

Dan Jacobson* and Guy Emerton

Author Affiliations

Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, 7600, South Africa

For all author emails, please log on.

BMC Bioinformatics 2012, 13:197  doi:10.1186/1471-2105-13-197

Published: 9 August 2012

Additional files

Additional file 1: Figure S1:

Percentage Variance Explained by each principal component.

Format: PDF Size: 187KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2: Figure S2:

Gene to Gene Distance Distribution.

Format: PDF Size: 162KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3: Figure S3:

Rank order distribution of the number of sets that each gene is contained in.

Format: PDF Size: 171KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4: Figure S4:

A) number of other gene sets that intersect with each gene set. B) Number of occurrences of gene overlaps between sets as found by set intersections.

Format: PDF Size: 212KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5: Figure S5:

Set sizes generated at each positive and negative arm of each principal component at thresholds 1, 5 and 10.

Format: PDF Size: 171KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

FunCat Enrichment of the False Negatives from traditional GSA pathway sets.

Format: GMT Size: 1.1MB Download file

Open Data

Additional file 7:

GO Enrichment (Biological Process) of the False Negatives from traditional GSA pathway sets.

Format: XLSX Size: 14KB Download file

Open Data

Additional file 8:

GO Enrichment (Molecular Function) of the False Negatives from traditional GSA pathway sets.

Format: XLSX Size: 19KB Download file

Open Data

Additional file 9:

GO Enrichment (Cellular Location) of the False Negatives from traditional GSA pathway sets.

Format: PDF Size: 753KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10:

Gene ID, Name and Description of metabolic genes found to be differentially expressed by GSA-PCA.

Format: PDF Size: 166KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 11:

The Gene Sets Generated with PCA Score Threshold 1.

Format: PDF Size: 118KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data