Graph-based iterative Group Analysis enhances microarray interpretation

Rainer Breitling¹^,2 , Anna Amtmann¹ and Pawel Herzyk²^,3

¹Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom

²Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, United Kingdom

³Sir Henry Wellcome Functional Genomics Facility, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom

author email corresponding author email

BMC Bioinformatics 2004, 5:100doi:10.1186/1471-2105-5-100


Published:	23 July 2004

Additional files

Additional File 1:

GiGA program. For use from the Windows command line.

Format: EXE Size: 671KB Download file

Additional File 2:

GiGA source code.

Format: PL Size: 15KB Download file

Additional File 3:

GiGA manual. Describes the use of GiGA applied to the example data (Additional files 4 to 6).

Format: PDF Size: 104KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 4:

Gene expression data. Sorted list of genes, based on expression during the yeast diauxic shift.

Format: TXT Size: 339KB Download file

Additional File 5:

Evidence network. List of gene pairs connecting genes whenever their gene products are enzymes that share a common substrate. Based on annotation derived from SwissProt.

Format: TXT Size: 957KB Download file

Additional File 6:

Genenames file. Contains descriptive names of the yeast genes contained in Additional file 4.

Format: TXT Size: 294KB Download file

Additional File 7:

Example output in text format. List of significantly affected subgraphs detected in the experimental data (Additional file 4) using GiGA with default settings.

Format: TXT Size: 5KB Download file

Additional File 8:

Example output in graph-description language format. Contains the same results as Additional file 7, but in a format that can be visualized and explored using graph-layout software, e.g. aiSee, which is freely available for academics at http://www.aisee.com webcite.

Format: GDL Size: 24KB Download file