The SVD (3, 4) and GSVD (5) cell cycle mRNA expression subspaces. (a) Normalized array correlation with the π/2-phase eigenarray along the y-axis vs. that with the 0-phase along the x-axis, color-coded according to the classification of the arrays into the five cell cycle stages by using combinatorics: M/G₁ (yellow), G₁ (green), S (blue), S/G₂ (red), and G₂/M (orange). The dashed unit and half-unit circles outline 100% and 25% of overall normalized array expression in this subspace. (b) Normalized correlation of each of the 646 cell cycle-regulated genes with the two corresponding eigengenes, color-coded according to either the traditional or microarray classifications. (c) The SVD picture of the yeast cell cycle. (d) Array expression, projected from the six-arraylets GSVD subspace onto π/2-phase along the y-axis vs. that onto 0-phase along the x-axis. The dashed unit and half-unit circles outline 100% and 50% of added up (rather than canceled out) contributions of the six arraylets to the overall projected expression. The arrows describe the projections of the –π/3-, 0-, and π/3-phase arraylets. (e) Expression of the 612 cell cycle-regulated genes, projected from the six-genelets GSVD subspace onto π/2-phase along the y-axis vs. that onto 0-phase along the x-axis. (f) The GSVD picture of the yeast cell cycle.

Pseudoinverse correlations of the proteins' DNA-binding data with the SVD (a and b) and GSVD (d and e) cell cycle mRNA expression bases. Shown are raster displays of ĉ ≡ b̂^†d̂, the correlations of the 13 binding profiles with the nine eigenarrays (a) and six arraylets (c) that span the SVD and GSVD bases, respectively. Also shown are line-joined graphs of the pseudoinverse correlations with the first (red) and second (blue) eigenarrays that span the SVD-cell cycle expression subspace (b), the third (red), fourth (blue), and fifth (green) arraylets (d), and the 14th (red), 15th (blue), and 16th (green) arraylets that span the GSVD cell cycle expression subspace (e).

Pseudoinverse reconstruction of the proteins' DNA-binding data in the SVD (a and b) and GSVD (c and d) cell cycle mRNA expression bases, with the ORFs sorted according to their SVD- and GSVD phases, respectively. Raster displays (a and c), with overexpression (red), no change in expression (black), and underexpression (green), and line-joined graphs (b and d) of the SVD- and GSVD-reconstructed 13 binding profiles along 2,227 and 2,139 ORFs, centered at their sample- and ORF-invariant levels, show a traveling wave in the nine transcription factors and a standing wave in the four replication initiation proteins.

Pseudoinverse mapping of the proteins' DNA-binding data onto the SVD (a) and GSVD (b) cell cycle mRNA expression subspaces. (a) Normalized sample correlation with the π/2-phase eigenarray along the y-axis vs. that with the 0-phase along the x-axis. (b) Sample binding projected from the six-arraylets GSVD subspace onto π/2-phase along the y-axis vs. that onto 0-phase along the x-axis.