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Open Access Highly Accessed Research article

Nutrient control of eukaryote cell growth: a systems biology study in yeast

Alex Gutteridge, Pınar Pir, Juan I Castrillo, Philip D Charles, Kathryn S Lilley and Stephen G Oliver*

Author Affiliations

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

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BMC Biology 2010, 8:68  doi:10.1186/1741-7007-8-68

Published: 24 May 2010

Additional files

Additional file 1:

Proteome/transcriptome correlation (carbon). Log. fold changes on increasing growth rate from D = 0.1 h-1 to D = 0.2 h-1 for protein (p) and gene expression (t) levels in carbon limitation.

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Additional file 2:

Proteome/transcriptome correlation (nitrogen). Log. fold changes on increasing growth rate from D = 0.1 h-1 to D = 0.2 h-1 for protein (p) and gene expression (t) levels in nitrogen limitation.

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Additional file 3:

Proteome/transcriptome correlation (phosphorus). Log. fold changes on increasing growth rate from D = 0.1 h-1 to D = 0.2 h-1 for protein (p) and gene expression (t) levels in phosphorus limitation.

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Additional file 4:

Proteome/transcriptome correlation (sulphur). Log. fold changes on increasing growth rate from D = 0.1 h-1 to D = 0.2 h-1 for protein (p) and gene expression (t) levels in sulphur limitation.

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Additional file 5:

GO, KEGG, Yeastract transcriptome/proteome analysis (carbon). Logistic regression results for carbon up/down regulated genes/proteins from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 119KB Download file

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Additional file 6:

GO, KEGG, Yeastract transcriptome/proteome analysis (nitrogen). Logistic regression results for nitrogen up/down regulated genes/proteins from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLSX Size: 93KB Download file

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Additional file 7:

GO, KEGG, Yeastract transcriptome/proteome analysis (phosphorus). Logistic regression results for phosphorus up/down regulated genes/proteins from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLSX Size: 78KB Download file

Open Data

Additional file 8:

GO, KEGG, Yeastract transcriptome/proteome analysis (sulphur). Logistic regression results for sulphur up/down regulated genes/proteins from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLSX Size: 102KB Download file

Open Data

Additional file 9:

Nutrient regulated GO biological process terms (transcriptome). GO biological process terms associated with up- (red) or down- (green) regulation of gene expression in one or more conditions (FDR < 1%).

Format: PDF Size: 86KB Download file

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Additional file 10:

Nutrient regulated GO molecular function terms (transcriptome). GO molecular function terms associated with up- (red) or down- (green) regulation of gene expression in one or more conditions (FDR < 1%).

Format: PDF Size: 16KB Download file

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Additional file 11:

Nutrient regulated GO cellular component terms (transcriptome). GO cellular component terms associated with up- (red) or down- (green) regulation of gene expression in one or more conditions (FDR < 1%).

Format: PDF Size: 44KB Download file

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Additional file 12:

Nutrient regulated GO biological process terms (proteome). GO biological process terms associated with up- (red) or down- (green) regulation of protein levels in one or more conditions (FDR < 1%).

Format: PDF Size: 45KB Download file

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Open Data

Additional file 13:

Nutrient regulated GO molecular function terms (proteome). GO molecular function terms associated with up- (red) or down- (green) regulation of protein levels in one or more conditions (FDR < 1%).

Format: PDF Size: 25KB Download file

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Additional file 14:

Nutrient regulated GO cellular component terms (proteome). GO cellular component terms associated with up- (red) or down- (green) regulation of protein levels in one or more conditions (FDR < 1%).

Format: PDF Size: 31KB Download file

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Open Data

Additional file 15:

Post-transcriptional control of YDR156W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YDR156W.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 16:

Post-transcriptional control of YLR174W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YLR174W.

Format: PDF Size: 324KB Download file

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Open Data

Additional file 17:

Post-transcriptional control of YBR142W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YBR142W.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 18:

Post-transcriptional control of YMR083W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YMR083W.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 19:

Post-transcriptional control of YHR087W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YHR087W.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 20:

Post-transcriptional control of YBR117C. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YBR177C.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 21:

Post-transcriptional control of YOL086C. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YOL086C.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 22:

Post-transcriptional control of YGL258W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YGL258W.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 23:

Post-transcriptional control of YDR345C. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YDR345C.

Format: PDF Size: 324KB Download file

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Open Data

Additional file 24:

Post-transcriptional control of YLR029C. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YL029C.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 25:

Post-transcriptional control of YJR152W. Protein and transcript log. fold changes in each nutrient-limiting condition relative to the overall mean for YJR152W.

Format: PDF Size: 324KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 26:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate carbon). Logistic regression results for growth rate up/down regulated genes/proteins in carbon limitation from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 132KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 27:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate nitrogen). Logistic regression results for growth rate up/down regulated genes/proteins in nitrogen limitation from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 148KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 28:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate phosphorus). Logistic regression results for growth rate up/down regulated genes/proteins in phosphorus limitation from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 145KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 29:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate sulphur). Logistic regression results for growth rate up/down regulated genes/proteins in sulphur limitation from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 147KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 30:

Growth rate regulated GO biological process terms (transcriptome). GO biological process terms associated with up- (red) or down- (green) regulation of gene expression with changes in growth rate in one or more conditions (FDR < 1%).

Format: PDF Size: 88KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 31:

Growth rate regulated GO molecular function terms (transcriptome). GO molecular function terms associated with up- (red) or down- (green) regulation of gene expression with changes in growth rate in one or more conditions (FDR < 1%).

Format: PDF Size: 28KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 32:

Growth rate regulated GO cellular component terms (transcriptome). GO cellular component terms associated with up- (red) or down- (green) regulation of gene expression with changes in growth rate in one or more conditions (FDR < 1%).

Format: PDF Size: 31KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 33:

Growth rate regulated GO biological process terms (proteome). GO biological process terms associated with up- (red) or down- (green) regulation of protein level with changes in growth rate in one or more conditions (FDR < 1%).

Format: PDF Size: 27KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 34:

Growth rate regulated GO molecular function terms (proteome). GO molecular function terms associated with up- (red) or down- (green) regulation of protein level with changes in growth rate in one or more conditions (FDR < 1%).

Format: PDF Size: 8KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 35:

Growth rate regulated GO cellular component terms (proteome). GO cellular component terms associated with up- (red) or down- (green) regulation of protein level with changes in growth rate in one or more conditions (FDR < 1%).

Format: PDF Size: 15KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 36:

ORFs under growth rate regulated post-transcriptional control. Individual genes that show significant changes in translational control efficiency between growth rates in each nutrient limitation. Colours indicate the log. ratio of translational control efficiency between the two growth rates. Only genes with a more than two-fold change in translational efficiency are shown.

Format: PDF Size: 34KB Download file

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Open Data

Additional file 37:

Post-transcriptional control of YPR184W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YPR184W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 38:

Post-transcriptional control of YLR034C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YLR034C.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 39:

Post-transcriptional control of YLR285W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YLR285W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 40:

Post-transcriptional control of YPR160W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YPR160W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 41:

Post-transcriptional control of YGR175C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YGR175C.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 42:

Post-transcriptional control of YOR303W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YOR303W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 43:

Post-transcriptional control of YDL171C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YDL171C.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 44:

Post-transcriptional control of YPL240C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YPL240C.

Format: PDF Size: 177KB Download file

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Open Data

Additional file 45:

Post-transcriptional control of YCL011C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YCL011C.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 46:

Post-transcriptional control of YGR087C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YGR087C.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 47:

Post-transcriptional control of YBR072W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YBR072W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 48:

Post-transcriptional control of YMR083W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YMR083W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 49:

Post-transcriptional control of YOL151W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YOL151W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 50:

Post-transcriptional control of YER021W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YER021W.

Format: PDF Size: 177KB Download file

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Open Data

Additional file 51:

Post-transcriptional control of YGL068W. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YGL068W.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 52:

Post-transcriptional control of YDR155C. Protein and transcript log. fold changes for the shift from D = 0.1 h-1 to D = 0.2 h-1 in each nutrient-limiting condition for YDR155C.

Format: PDF Size: 177KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 53:

Physiological parameters. Specific rates of glucose comsumption (qgluc) and ethanol production (qethanol) from the chemostat series under specific nutrient-limiting conditions.

Format: DOC Size: 38KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 54:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate carbon specific). Logistic regression results for growth rate up/down regulated genes/proteins in carbon limitation relative to the overall growth rate effect from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 81KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 55:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate nitrogen specific). Logistic regression results for growth rate up/down regulated genes/proteins in nitrogen limitation relative to the overall growth rate effect from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 52KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 56:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate phosphorus specific). Logistic regression results for growth rate up/down regulated genes/proteins in phosphorus limitation relative to the overall growth rate effect from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 53KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 57:

GO, KEGG, Yeastract transcriptome/proteome analysis (growth rate sulphur specific). Logistic regression results for growth rate up/down regulated genes/proteins in sulphur limitation relative to the overall growth rate effect from the transcriptome (trans) and proteome (prot) data using GO, KEGG and Yeastract annotations.

Format: XLS Size: 39KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 58:

Nutrient specific growth rate regulated GO biological process terms (transcriptome). GO biological process terms associated with up- (red) or down- (green) regulation of gene expression with increasing growth rate in one or more conditions relative to the overall trend (FDR < 1%).

Format: PDF Size: 34KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 59:

Nutrient specific growth rate regulated GO molecular function terms (transcriptome). GO molecular function terms associated with up- (red) or down- (green) regulation of gene expression with increasing growth rate in one or more conditions relative to the overall trend (FDR < 1%).

Format: PDF Size: 9KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 60:

Nutrient specific growth rate regulated GO cellular component terms (transcriptome). GO cellular component terms associated with up- (red) or down- (green) regulation of gene expression with increasing growth rate in one or more conditions relative to the overall trend (FDR < 1%).

Format: PDF Size: 21KB Download file

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Open Data

Additional file 61:

Logistic regression example. Association of positive slopes of regression with the ribosome biogenesis GO term. Slopes are calculated for each gene from a linear regression of gene expression against growth rate. Vertical tick marks show the slopes of ribosome biogenesis annotated genes. The proportion of all genes at a given slope that are annotated with the term is shown with the dashed line. The solid line shows the fitted logistic regression.

Format: PDF Size: 9KB Download file

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Open Data