Open Access Research article

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Nathan L Tintle1*, Alexandra Sitarik2, Benjamin Boerema3, Kylie Young4, Aaron A Best5 and Matthew DeJongh6

Author Affiliations

1 Department of Mathematics, Statistics and Computer Science, Dordt College, Sioux Center, IA, 51250, USA

2 Department of Biostatistics, University of Michigan, Ann Arbor, MI, 43109, USA

3 Department of Industrial and Operations Engineering, University of Michigan, Ann Arbor, MI, 48109, USA

4 Department of Mathematics, Hope College, Holland, MI, 49423, USA

5 Department of Biology, Hope College, Holland, MI, 49423, USA

6 Department of Computer Science, Hope College, Holland, MI, 49423, USA

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BMC Bioinformatics 2012, 13:193  doi:10.1186/1471-2105-13-193

Published: 8 August 2012

Additional files

Additional file 1:

Table S1. Marginal effects of source in models controlling for set size only.

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Additional file 2:

Table S2. Marginal effects of source in models controlling for set size and organism.

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Additional file 3:

Table S3. Model r2 when controlling for set size and organism.

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Additional file 4:

Table S4. Mean levels of consistency by source when sets are reduced to only contain genes that are contained in at least one SEED path.

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Additional file 5:

Table S5. Mean levels of consistency by source when sets are reduced to only contain genes that are contained in at least one predicted operon.

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Additional file 6:

Table S6. Gene set consistency characteristics for sets associated with arginine biosynthesis.

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Additional file 7:

Figure S1. Pairwise correlations between genes in arginine biosynthesis.

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