Supplementary Figures S1 : Principal Component Analysis (PCA) of the S. pombe and S. cerevisiae time course sporulation data Supplementary Figure S2 : 3D-gene expression networks derived from randomized data Supplementary Figure S3 : Visualization of the temporal gene activation Supplementary Note S4 : Gene repartition in the four temporal classes Supplementary Figures S5 : Result of the superimposition with a w-value = 0 Supplementary Note S6 : Optimisation result and significance Supplementary Figure S7: Direct comparison of the gene expression profiles for orthologous pairs Supplementary Note S8: Conservation of expression between organisms can be used for improving functional gene annotation Supplementary Note S9 : Co-expression can be used for refining orthologous links between organisms Supplementary Note S10: Assessment of the approach with simulated data with known effects Supplementary Note S11 : Comparison of cell-cycle gene expression programs between budding and fission yeasts Supplementary Note S12: Hidden relationships between sporulation-induced genes

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