S1. Supplementary data for Fig. 1:

Short description: filtered genes during growth using as criteria P-call  1 and at least 2 FC in expression after comparative analysis

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: P_call (total of detected present calls by MASuite5.0)
  4. column: NC_call (total of detected “no change” calls by MASuite5.0)
  5. column: Self organising map analysis result indicating the appearance in specific cluster model (c1-c6_growth)
  6. column: hierarchical tree analysis result indicating the position on branch (growth_node A-B)
  7. column: maximum detected fold change (max FC) after comparative analysis against the sample taken at day 7

S2. Supplementary data for Fig. 3:

Short description: filtered genes after sucrose using as criteria P-call  1 and at least 2 FC in expression after comparative analysis

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: P_call (total of detected present calls by MASuite5.0)
  4. column: NC_call (total of detected “no change” calls by MASuite5.0)
  5. column: Self organising map analysis (SOM) result indicating the appearance in specific cluster model (c1-c12_suc)
  6. column: defined pattern of expression after SOM analysis (up-regulation, down-regulation, re-entry)
  7. column: hierarchical tree analysis result indicating the position on branch (suc_node A-C)
  8. column: maximum detected fold change (max FC) after comparative analysis against the sample taken after starvation (T0)

S3. Supplementary data for Fig. 5 (comparison 8K_ATH1-array):

  1. column: gene identifier (MIPS ID as released by TAIR)
  2. column: probe set ID (probe identifier by Affymetrix; 8K-array)
  3. column: probe set ID (probe identifier by Affymetrix; ATH1-array)
  4. column: p1-value (value for period fluctuation after statistic analysis using the 8K-array)
  5. column: p2-value (value for period fluctuation after statistic analysis using the ATH1-array)
  6. column: SQRT (p1p2) (root square of the product of p1-value (8K-array) multiplied with p2-value (ATH1-array)

S4. Supplementary data for Fig. 6:

Short description: filtered genes after aphidicolin treatment after statistical analysis (p<0.05) and applying as criteria at least a 2 FC after comparative analysis

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: P_call (total of detected present calls by MASuite5.0)
  4. column: NC_call (total of detected “no change” calls by MASuite5.0)
  5. column: Self organising map analysis result indicating the appearance in specific cluster model (c1-c16_aph)
  6. column: hierarchical tree analysis result indicating the position on branch (aph_node A-G)
  7. column: peak, definition of phase peak (based on absolute detected signals)
  8. column: Peak (observed), numerical characterisation of sinusoidal expression (phase (hrs)) after statistical analysis
  9. column: p-value (value for period fluctuation after statistic analysis using the ATH1-array)
  10. column: maximum detected fold change (max FC) after comparative analysis against the sample taken after block release

S5. Supplementary data for Fig. 7

Short description: filtered genes after aphidicolin treatment using as criteria P-call  3 and at least 3 FC after comparative analysis (data set B: 1,484)

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: P_call (total of detected present calls by MASuite5.0)
  4. column: NC_call (total of detected “no change” calls by MASuite5.0)
  5. column: peak, definition of phase peak (based on absolute detected signals)
  6. column: comparison to data set A (designated as “present in A” if gene was also defined as cell cycle regulated after statistical analysis)
  7. column: growth filter (designated as “yes” if gene passed the applied growth-filter)
  8. column: sucrose filter (designated as “yes” if gene passed the applied sucrose-filter for data set B)
  9. column: maximum detected fold change (max FC) after comparative analysis against the sample taken after block release

S6. Supplementary data for sucrose-unique genes

Short description: filtered genes after comparative analysis that show expression and regulation during cell cycle re-entry, but are not expressed during cell cycle progression (aphidicolin) and growth.

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: description field (annotation)
  4. column: P_call (total of detected present calls by MASuite5.0)
  5. column: NC_call (total of detected “no change” calls by MASuite5.0)
  6. column: Self organising map analysis (SOM) result indicating the appearance in specific cluster model (c1-c12_suc)
  7. column: defined pattern of expression after SOM analysis (up-regulation, down-regulation, re-entry)
  8. column: hierarchical tree analysis result indicating the position on branch (suc_node A-C)

S7. Supplementary data for putative stress-related or quiescence associated genes

Short description: filtered genes after comparative analysis, which are expressed after starvation (T0), but not in stationary phase cell suspension (D7).

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: description field (annotation)
  4. column: “detection” call after starvation (T0) (P = present; A = absent; MASuite5.0)
  5. column: “detection” call in stationary phase (D7) (P = present; A = absent; MASuite5.0)
  6. column: Signal Log Ratio after comparative analysis of sample T0 (after sucrose starvation) using stationary growth sample (D7) as baseline (MASuite5.0)
  7. column: “change” call after comparative analysis of sample T0 (after sucrose starvation) using stationary growth sample (D7) as baseline (MASuite5.0)
  8. column: P_call during re-entry experiment (sucrose) (total of detected present calls by MASuite5.0)
  9. column: Self organising map analysis (SOM) result indicating the appearance in specific cluster model (c1-c12_suc) during cell cycle re-entry
  10. column: defined pattern of expression after SOM analysis (up-regulation, down-regulation, re-entry) during cell cycle re-entry
  11. column: hierarchical tree analysis result indicating the position on branch (suc_node A-C) during cell cycle re-entry
  12. column: P_call during growth experiment (total of detected present calls by MASuite5.0)
  13. column: Self organising map analysis result indicating the appearance in specific cluster model (c1-c6_growth) during unperturbed growth
  14. column: hierarchical tree analysis result indicating the position on branch (growth_node A-B) during unperturbed growth

S8. Supplementary data for putative starvation responsive genes, which might switch off metabolism in response to sucrose starvation and re-activate gene expression during cell cycle re-entry.

Short description: filtered genes after comparative analysis, which are expressed in stationary phase cell suspension (D7), but not after starvation (T0).

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: description field (annotation)
  4. column: “detection” call after starvation (T0) (P = present; A = absent; MASuite5.0)
  5. column: “detection” call in stationary phase (D7) (P = present; A = absent; MASuite5.0)
  6. column: Signal Log Ratio after comparative analysis of sample T0 (after sucrose starvation) using stationary growth sample (D7) as baseline (MASuite5.0)
  7. column: “change” call after comparative analysis of sample T0 (after sucrose starvation) using stationary growth sample (D7) as baseline (MASuite5.0)
  8. column: P_call during re-entry experiment (sucrose) (total of detected present calls by MASuite5.0)
  9. column: Self organising map analysis (SOM) result indicating the appearance in specific cluster model (c1-c12_suc) during cell cycle re-entry
  10. column: defined pattern of expression after SOM analysis (up-regulation, down-regulation, re-entry) during cell cycle re-entry
  11. column: hierarchical tree analysis result indicating the position on branch (suc_node A-C) during cell cycle re-entry
  12. column: P_call during growth experiment (total of detected present calls by MASuite5.0)
  13. column: Self organising map analysis result indicating the appearance in specific cluster model (c1-c6_growth) during unperturbed growth
  14. column: hierarchical tree analysis result indicating the position on branch (growth_node A-B) during unperturbed growth

S9. Supplementary data for putative stationary phase-related genes.

Short description: filtered genes after comparative analysis, which are expressed in stationary phase cell suspension (D7), but not in early lag phase after subculture into fresh medium (D1).

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: description field (annotation)
  4. column: “detection” call in early lag phase (D1) (P = present; A = absent; MASuite5.0)
  5. column: “detection” call in stationary phase (D7) (P = present; A = absent; MASuite5.0)
  6. column: Signal Log Ratio after comparative analysis of sample D7 (stationary) using sample D1 (early lag phase) as baseline (MASuite5.0)
  7. column: “change” call after comparative analysis of sample D7 (stationary) using sample D1 (early lag phase) as baseline (MASuite5.0)
  8. column: P_call during growth experiment (total of detected present calls by MASuite5.0)
  9. column: Self organising map analysis result indicating the appearance in specific cluster model (c1-c6_growth) during unperturbed growth
  10. column: hierarchical tree analysis result indicating the position on branch (growth_node A-B) during unperturbed growth

S10. Supplementary data for putative subculture or sugar responsive genes.

Short description: filtered genes after comparative analysis, which are expressed in early lag phase after subculture into fresh medium (D1), but not in stationary phase cell suspension (D7).

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: description field (annotation)
  4. column: “detection” call in early lag phase (D1) (P = present; A = absent; MASuite5.0)
  5. column: “detection” call in stationary phase (D7) (P = present; A = absent; MASuite5.0)
  6. column: Signal Log Ratio after comparative analysis of sample D7 (stationary) using sample D1 (early lag phase) as baseline (MASuite5.0)
  7. column: “change” call after comparative analysis of sample D7 (stationary) using sample D1 (early lag phase) as baseline (MASuite5.0)
  8. column: P_call during growth experiment (total of detected present calls by MASuite5.0)
  9. column: Self organising map analysis result indicating the appearance in specific cluster model (c1-c6_growth) during unperturbed growth
  10. column: hierarchical tree analysis result indicating the position on branch (growth_node A-B) during unperturbed growth

S11. Supplementary data for putative stress-related or aphidicolin-induced genes

Short description: removed genes that didn’t pass applied filter after combinatorial analysis as described in discussion for Figure 7.

  1. column: probe set ID (probe identifier by Affymetrix)
  2. column: gene identifier (MIPS ID as released by TAIR)
  3. column: description field (annotation)
  4. column: removal from dataset by applied “growth filter” or “sucrose filter”

S12. Supplementary data for table 2

Short description: identified genes showing cell cycle regulated and cell cycle associated expression (including unknown, putative, hypothetical and expressed proteins)

As described in table legend (manuscript)