Methodology article
Gene set analyses for interpreting microarray experiments on prokaryotic organisms
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* Corresponding author: Nathan L Tintle tintle@hope.edu
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
BMC Bioinformatics 2008, 9:469 doi:10.1186/1471-2105-9-469
Published: 5 November 2008Additional 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
This file can be viewed with: Adobe Acrobat Reader
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
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
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
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