S extremely equivalent across the 3 S. cerevisiae cellcycle profiling experiments.
S very comparable across the three S. cerevisiae cellcycle profiling experiments. (TIF) S5 Fig. A core set of about 00 orthologous fungal genes is conserved in periodicity and in temporal expression among Saccharomyces cerevisiae, Cryptococcus neoformans, and Candida albicans. A list of 494 periodic genes in C. albicans was obtained from Cote et al 2009 [49]. Applying FungiDB, the Candida Genome Database (CGD), plus the original publication’s Supplemental Table , the C. albicans genes had been mapped to 504 S. cerevisiae orthologs [46,49,8]. This PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26365614 C. albicans . cerevisiae list was crossed using the S. cerevisiae . neoformans orthologous, top periodic gene list from Fig 3. The final lists of S. cerevisiae . neoformans . albicans orthologs are shown right here. The 96 exceptional S. cerevisiae genes are ordered on peak time expression, as in Fig three (A). The 89 unique C. neoformans genes (B) are ordered the same as their respective ortholog in a. Four replicates of microarray time series data in the C. albicans cell cycle have been averaged together for the 92 special probe IDs of interest, excluding missing information points, applying R (C). In each heatmap, transcript levels are depicted as a zscore change relative to mean expression for every single gene, where values represent the amount of normal deviations away in the mean. Every single row represents an orthologous periodic gene set, within the same order for (AC) (for precise ordering of gene pairs and multiplemappings, see S5 Table, Tab 2). (TIF)PLOS Genetics DOI:0.37journal.pgen.006453 December 5,7 CellCycleRegulated ZL006 Transcription in C. neoformansS6 Fig. CLOCCS model fits and parameter estimates for aligning the time series data. The first, most synchronous cycle of budding information from S. cerevisiae and C. neoformans (Fig ) was fed in to the CLOCCS model [59,60]. The fraction of cells having a bud (filled circles) is shown for S. cerevisiae (blue) and C. neoformans (green) wildtype cells (A, reproduced from Fig ). The CLOCCS predicted firstbud curves and connected uncertainty (purple band) is shown for S. cerevisiae and C. neoformans, respectively (CD). The CLOCCS parameters are provided in a table for each and every experiment, which contains the imply value and 95 self-confidence interval (in parentheses) for each model parameter (E). The mean values for cellcycle period and recovery time (0) have been utilized to align the two time series (Figs 4 and six) by converting time points to scaled CLOCCS lifeline points (see S File). The scaled budding curves, aligned by CLOCCS lifeline points, are also shown here (B). (TIF) S7 Fig. Quantification of peak occasions for budding, DNA replication, spindle assembly, and mitosis genes in S. cerevisiae and C. neoformans shown in Fig four. Peak expression occasions for cellcycle genes and orthologs in S. cerevisiae (blue) and C. neoformans (green) have been found in the 1st cell cycle (see Fig 4A, 4B, 4D, 4E, 4G and 4H). Cycle gene expression peak occasions have been also discovered inside the frequent cellcycle timeline (CLOCCS lifeline point units) as described (see S File). Histograms of peak instances for S. cerevisiae periodic budding genes (77) and orthologous C. neoformans genes (6) show peaks distributed all through the initial cell cycle (AB). Histograms of peak times for S. cerevisiae periodic DNA replication genes (six) and orthologous C. neoformans genes (53) show a tight distribution of peak occasions within the midcell cycle and comparable temporal ordering in between the two yeasts (CD). Histograms of peak occasions for S. cerevisiae periodic mitosis genes (43) and or.
