Fig. 3: Cell cycle phase specific processes.
A Classification of the strongly differentially expressed genes in each pair-wise comparison by arCOG category. Genes were annotated and classified using the arCOG framework (see Methods). Genes included in the graph were only those strongly differentially expressed, i.e., their fold change (FC) was at least ±2 and their adjusted p value was <0.01. Statistical significance is extracted from the DGE analysis (Supplementary Data 1), where it was calculated with the limma package and p values were adjusted for multiple comparisons using the Benjamini-Hochberg method. The number of genes is shown on the x-axis, genes to the right of the vertical axis are upregulated in the corresponding comparison, while genes to the left are downregulated. B Specific co-expression during the S phase. GCN of the S phase with the specific nodes highlighted, grouped and colored by arCOG category (see Supplementary Fig. S5 for GCNs of the M-G1 and G2 phases). C Differences in the metabolism between phases. A full metabolic map of S. islandicus was extracted from the KEGG database94 (accession number: sir01100 [https://www.kegg.jp/pathway/sir01100]). Each dot represents a metabolite while each line represents the enzymes that transform those metabolites. Each pathway is classified into six groups depending on their peak of activity according to the KEGG enrichment and DGE analysis: (i) ‘All’, if their activity does not change, (ii) ‘M-G1’, (iii) ‘S’ or (iv) ‘G2’, if their activity peaks at each of the corresponding phases, and (v) ‘M-G1/S’ or (vi) ‘S/G2’, if their activity increased at the M-G1 or S phases and was maintained high into the following phase. Different pathways of interest are labeled on the map next to their metabolites.
