Yeast and human genelets. (a) Raster display of x̂⁻¹, the expression of 18 genelets in 18 yeast and human arrays simultaneously, centered at their array-invariant levels. (b) Bar chart of the angular distances showing 〈γ₁| and 〈γ₂| highly significant in the yeast data relative to the human data, 〈γ₃|, 〈γ₄|, 〈γ₅|, 〈γ₆|, 〈γ₁₄|, 〈γ₁₅|, and 〈γ₁₆| almost equally significant in both data sets and 〈γ₁₇| and 〈γ₁₈| highly significant in the human data relative to the yeast data. All other genelets are significant in neither the yeast data nor the human data (see Appendix).

Line-joined graphs of the expression levels of the genelets. (a) 〈γ₃| (red), 〈γ₄| (blue), and 〈γ₅| (green), which are associated with the common yeast and human cell-cycle gene-expression oscillations, fit dashed graphs of normalized cosines of two periods and initial phases of π/3 (red), 0 (blue), and −π/3 (green), respectively. (b) 〈γ₁₄| (red), 〈γ₁₅| (blue), and 〈γ₁₆| (green), which also are associated with cell-cycle gene-expression oscillations, fit dashed graphs of normalized cosines of two and a half periods and initial phases of −π/3 (red), π/3 (blue), and 0 (green), respectively. (c) 〈γ₁| (red) and 〈γ₂| (blue) are associated with the exclusive yeast pheromone response, 〈γ₁₇| (orange) and 〈γ₁₈| (green) are associated with the exclusive human stress response, and 〈γ₆| (violet) is associated with both the yeast and human transitions from synchronization response into the cell cycle.

Yeast (a–d) and human (e–h) expression reconstructed in the six-dimensional cell-cycle subspaces with genes sorted according to their phases in the two-dimensional subspaces that approximate them. (a) Yeast expression of the sorted 4,523 genes in the 18 arrays, centered at their gene- and array-invariant levels, showing a traveling wave of expression. (b) Yeast expression of the sorted 4,523 genes in the 18 arraylets, centered at their array-invariant levels. The expression of the arraylets |α_1,3〉, |α_1,4〉, |α_1,5〉, |α_1,14〉, |α_1,15〉, and |α_1,16〉 displays the sorting. (c) Yeast cell-cycle arraylet expression levels |α_1,3〉 (red), |α_1,4〉 (blue), and |α_1,5〉 (green) fit one-period cosines of π/3 (red), 0 (blue), and −π/3 (green) initial phases. (d) Yeast cell-cycle arraylet expression levels |α_1,14〉 (red), |α_1,15〉 (blue), and |α_1,16〉 (green) fit one-period cosines of −π/3 (red), π/3 (blue), and 0 (green) initial phases. (e) Human expression of the sorted 12,056 genes in the 18 arrays centered at their gene- and array-invariant levels showing a traveling wave of expression. (f) Human expression of the sorted 12,056 genes in the 18 arraylets centered at their array-invariant levels. The expression of the arraylets |α_2,3〉, |α_2,4〉, |α_2,5〉, |α_2,14〉, |α_2,15〉 and |α_2,16〉 displays the sorting. (g) Human cell-cycle arraylet expression levels |α_2,3〉 (red), |α_2,4〉 (blue), and |α_2,5〉 (green) fit one-period cosines of π/3 (red), 0 (blue), and −π/3 (green) initial phases. (h) Human cell-cycle arraylet expression levels |α_2,14〉 (red), |α_2,15〉 (blue), and |α_2,16〉 (green) fit one-period cosines of −π/3 (red), π/3 (blue), and 0 (green) initial phases.

Yeast (a–c) and human (d–f) expression reconstructed in the six-dimensional cell-cycle subspaces approximated by two-dimensional subspaces. (a) Yeast array expression, projected onto π/2-phase along the y axis vs. that onto 0-phase along the x axis and color-coded according to the classification of the arrays into the five cell-cycle stages: M/G₁ (yellow), G₁ (green), S (blue), S/G₂ (red), and G₂/M (orange). 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. (b) Yeast expression of 603 cell cycle-regulated genes projected onto π/2-phase along the y axis vs. that onto 0-phase along the x axis and color-coded according to the classification by Spellman et al. (11) (c) Yeast expression of 76 cell cycle-regulated genes color-coded according to the traditional classification. (d) Human array expression color-coded according to the classification of the arrays into the five cell-cycle stages: S (blue), G₂ (red), G₂/M (orange), M/G₁ (yellow), and G₁/S (green). (e) Human expression of 750 cell cycle-regulated genes color-coded according to the classification by Whitfield et al. (12) (f) Human expression of 73 cell cycle-regulated genes color-coded according to the traditional classification; the arrows point to 16 human histones that were not classified by Whitfield et al. as cell cycle-regulated based on their overall expression.