Open Access Highly Accessed Methodology article

Gene set analyses for interpreting microarray experiments on prokaryotic organisms

Nathan L Tintle1*, Aaron A Best2, Matthew DeJongh3, Dirk Van Bruggen13, Fred Heffron4, Steffen Porwollik5 and Ronald C Taylor6

Author Affiliations

1 Department of Mathematics, Hope College, Holland, Michigan, USA

2 Department of Biology, Hope College, Holland, Michigan, USA

3 Department of Computer Science, Hope College, Holland, Michigan, USA

4 Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA

5 Sidney Kimmel Cancer Center, San Diego, California, USA

6 Computational Biology & Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA

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BMC Bioinformatics 2008, 9:469  doi:10.1186/1471-2105-9-469

Published: 5 November 2008

Additional files

Additional file 1:

Significant gene sets for the 18 experiments. A listing of the significant gene sets found by FET 1, FET 1/2, ABSSUM-NR, SUM-NR and MAXMEAN-NR for each of the 18 experiments, along with summary statistics for the distribution of log-ratios of expression values within each set.

Format: PDF Size: 128KB Download file

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Additional file 2:

Gene set definitions for E. coli. This is a tab-delimited file with 4290 rows (one for each gene) and 338 columns. The first column gives the gene ID (b-number); the remaining 337 indicate whether (1) or not (0) the gene is in the gene set. There are 337 gene sets for E. coli based on SEED subsystems.

Format: DAT Size: 2.8MB Download file

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Additional file 3:

Gene set names for E. coli. This is a tab-delimited file with 337 rows (one for each gene set) and 3 columns. The first column is the SEED subsystem name, the second is the numeric identifier for the set (1–337; corresponds to the order of sets in Additional file #2), and the third column indicates the number of genes in the set.

Format: TXT Size: 12KB Download file

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Additional file 4:

Gene set definitions for S. typhimurium. This is a tab-delimited file with 4493 rows (one for each gene) and 332 columns. The first column gives the gene ID (STM number); the remaining 331 indicate whether (1) or not (0) the gene is in the gene set. There are 331 gene sets for S. typhimurium based on SEED subsystems.

Format: DAT Size: 2.9MB Download file

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Additional file 5:

Gene set names for S. typhimurium. This is a tab-delimited file with 331 rows (one for each gene set) and 3 columns. The first column is the SEED subsystem name, the second is the numeric identifier for the set (1–331; corresponds to the order of sets in Additional file #4), and the third column indicates the number of genes in the set.

Format: TXT Size: 12KB Download file

Open Data