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Open Access Highly Accessed Research article

The genetic control of growth rate: a systems biology study in yeast

Pınar Pir1, Alex Gutteridge1, Jian Wu2, Bharat Rash2, Douglas B Kell3, Nianshu Zhang1 and Stephen G Oliver1*

Author Affiliations

1 Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK

2 Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK

3 Manchester Interdisciplinary Biocentre and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK

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BMC Systems Biology 2012, 6:4  doi:10.1186/1752-0509-6-4

Published: 13 January 2012

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Additional file 1:

Additional Text and Methods. Additional text on results and details on methods are provided.

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Additional file 2:

Figure S1. Histogram of relative growth rates (FCC') of HFC genes and all genes in turbidostats. HI: Haploinsufficient, HP: Haploproficient (FDR < 0.05 is the threshold for significant HI and HP genes). FCC's of 5713 genes (genome), 1932 HI genes and 796 HP genes were binned into 50 intervals each.

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Additional file 3:

Table S1: Relative growth rates from the experiments. Abbreviations: C, N, P: Carbon-, Nitrogen- or Phosphorus-limited F1 media 01, 02, 03: Dilution rates in chemostats of 0.1, 0.2 or 0.3 h-1, respectively Turb: Turbidostat FPM: Footprinting media Columns: 1: Systematic name of the ORF, one copy of which has been deleted in the hemizygous diploids All columns denoted as .FCC': Relative growth rate (modified control coefficient) of the mutant in the corresponding experiment. All columns denoted as .P: P-value for rejecting the hypothesis that GR ≠ 0. All columns denoted as .FDR: False discovery rate at the specified P-value.

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Additional file 4:

Table S2: GO analysis of the growth rates. Each experiment is given on a separate spreadsheet. Abbreviations: C, N, P: Carbon-, Nitrogen- or Phosphorus-limited F1 media 01, 02, 03: Dilution rates in chemostats of 0.1, 0.2 or 0.3 h-1, respectively Turb: Turbidostat FPM: Footprinting media Columns: 1: Internal database row number. 2: GO term ID 3: Name of the GO term 4: Class of the GO term (MF: Molecular Function, BP: Biological Process, CC: Cellular Compartment) 5: Number of genes annotated to the GO term 6: Coeff: Logistic regression coefficient β of the GO term. Positive values indicate enrichment of a GO term among the haploproficient genes, negative values indicate enrichment among the haploinsufficient genes. 7: Odd.ratio: Log odds ratio of the GO term. 8: P-value: P-value for rejecting the null hypothesis that β≠0 9: FDR: False Discovery Rate at specified P-value.

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Additional file 5:

Figure S2. Fraction of HFC genes related to selected organelles, protein complexes, and cellular processes. Only genes showing an HFC phenotype in turbidostat culture are considered. The key on the top left gives the colour code used in the chart: Dark blue gives the percent of significantly HI (FDR < 0.05) and dark red gives the percent of significantly HP (FDR < 0.05).

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Additional file 6:

Table S3: Haploproficient genes involved in the maintenance of genome integrity. Columns: 1. ORF name 2. Gene name 3. Gene description 4. Relative growth rates (FCC') 5. FDR: False Discovery Rate.

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