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High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

Barry R Zeeberg* 1 email, Haiying Qin* 2 email, Sudarshan Narasimhan3 email, Margot Sunshine3 email, Hong Cao3 email, David W Kane3 email, Mark Reimers3 email, Robert M Stephens4 email, David Bryant4 email, Stanley K Burt4 email, Eldad Elnekave5 email, Danielle M Hari5 email, Thomas A Wynn5 email, Charlotte Cunningham-Rundles6 email, Donn M Stewart2 email, David Nelson2 email and John N Weinstein1 email

1Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

2Metabolism Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

3SRA International, 4300 Fair Lakes CT, Fairfax, VA 22033, USA

4Advanced Biomedical Computing Center, National Cancer Institute at Frederick, SAIC Frederick, PO Box B, Frederick, MD, 21702, USA

5Laboratory of Parasitic Disease, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA

6The Mount Sinai Medical Center, 1425 Madison Avenue, New York, NY 10029, USA

author email corresponding author email* Contributed equally

BMC Bioinformatics 2005, 6:168doi:10.1186/1471-2105-6-168

Published: 5 July 2005

Additional files

Additional File 1:

Stability of Estimates of the False Discovery Rate

Format: XLS Size: 1KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 2:

Expression Data

Format: XLS Size: 1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 3:

Output Files Generated from High-Throughput GoMiner

Format: TAR Size: 2.8MB Download file

Additional File 4:

Methodology Description

Format: TXT Size: 4KB Download file

Additional File 6:

Summary Report

Format: XLS Size: 505KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 7:

Gene Category Report

Format: XLS Size: 225KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 8:

CIM of Transcription Factors versus GO Categories

Format: PDF Size: 294KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 9:

Discussion of Results

Format: TXT Size: 3KB Download file

Additional File 5:

Instructions for Generating the CIMs in the Manuscript

Format: PDF Size: 275KB Download file

This file can be viewed with: Adobe Acrobat Reader


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