Research article
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
1 Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, USA
2 Department of Biostatistics, University of California, Berkeley, CA, USA
3 Department of Radiology, University of Washington, WA, USA
4 Department of Applied Science, University of California, Davis, USA
BMC Bioinformatics 2006, 7:381 doi:10.1186/1471-2105-7-381
Published: 16 August 2006Additional files
Additional File 1:
Transcription factor network of canonical cell cycle regulators as derived from the cdc15 time course. We show the non-zero entries in the model's time-translation matrix as directed arcs between transcription factors. We note the general similarity of the causal flow in this network to Figure 3 which was derived from the mating pheromone arrest time course. The order of factors displayed here minimizes the number of upward arcs (these arcs being grouped on the right side).
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Additional File 2:
Transcription factor network of canonical cell cycle regulators as derived from the elutriation time course. We show the non-zero entries in the model's time-translation matrix as directed arcs between transcription factors. We note the general similarity of the causal flow in this network to Figure 3 which was derived from the mating pheromone arrest time course. The order of factors displayed here minimizes the number of upward arcs (these arcs being grouped on the right side).
Format: TIFF Size: 908KB Download file
Additional File 3:
α-coefficients of transcription factors regulating the cell cycle. A heat map (in the style of Figure 2) of the α-coefficients of the transcription factors from our extended 12-factor model during two periods of the cell cycle.
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Additional File 4:
Transcription factor rankings used to select the 4 non-canonical transcription factors. Factors were ranked based on the number of time points in which their p-values were significant beyond some threshold (p < 0.1, 0.01, or 0.001). They were further ranked based on the periodicity of their α-coefficients. Canonical factors are shown in red, significant non-canonical factors are shown in yellow, and other factors are shown in white. We see that the same set of 5 non-canonical factors is selected as most significant for all of the p-value thresholds.
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Additional File 5:
Eigenvalues of the time-translation matrix of the 12-factor model. Each application of the time-translation matrix moves time forward 7 minutes.
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Additional File 6:
Asymptotic phases and amplitudes. A derivation of the formulas used for the asymptotic phases and amplitudes of components of real systems governed by a general class of real time-translation matrices is given.
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