Research
Metabolic-network-driven analysis of bacterial ecological strategies
- † Equal contributors
1 The Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
2 School of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
3 School of Mathematical Science, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
4 Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
5 Santa Fe Institute, Santa Fe, NM 87501, USA
6 Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
Genome Biology 2009, 10:R61 doi:10.1186/gb-2009-10-6-r61
Published: 5 June 2009Additional files
Additional data file 1:
Genomic and ecological attributes for the 113 species in the analysis.
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Additional data file 2:
NCBI annotations and description of environmental samples for species that can be identified in an environmental sample.
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Additional data file 3:
Supplementary notes and figures, detailed description of all tables in the Additional data files and a table. Table S5: Correlation (P value) versus duplication time in random environments. Figure S1: Distribution of the correlations between doubling time and ESI and maximal-CHS in random samples of species selected in a way that allows equal number of representatives for each ecological habitat. Figure S2: Distribution of the correlations between doubling time and ESI and maximal-CHS in random samples of species selected in a way that allows a single representative for each taxonomic group. Figure S3: The distribution of Pearson correlation coefficients of the ESI values with randomized maximal CHS values. Figure S4: General distribution of species/environment in 3 different sets of environments (original and random). Figure S5: Mean maximal CHS levels of bacteria of a given life style. Figure S6: The distribution of log doubling time of the 113 species studied. Figure S7: The mean and standard deviation of the recoever operating characteristics (ROC) curve obtained in 50 cross validation experiments.
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Additional data file 4:
Original and manually curated values of environmental complexity.
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Additional data file 5:
Biomass target metabolites.
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Additional data file 6:
Genomic and ecological attributes for the 528 species in the metabolic analysis.
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