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Supplementary Figure S1.
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Unsupervised clustering analysis using Firehose of RNA-seq data from TCGA breast
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cancer transcriptomes, identifying 7 sample clusters.
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Supplementary Figure S2.
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(A) GO analysis (by DAVID) of the 100 genes whose expression is most highly correlated
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with that of Ki-67, as determined by COEXPRESdb.
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(B) Correlation between cyclin-annotated genes and Ki-67 across colorectal cancer
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subtypes.
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(C) Histogram of the number of Ki-67 significantly correlated genes in TCGA breast
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tumours with respect to Spearman correlation values (all correlation adjusted P < 0.05).
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The upper right bar plots report the proportion and number of cell cycle genes among
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genes above a certain correlation coefficient.
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(D) Correlation between cancer-annotated genes and Ki-67 across TCGA breast cancer
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subtypes.
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Supplementary Figure S3. Cell cycle dynamics of Ki-67 expression are similar in
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non-transformed cells and cancer cell lines.
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A. Immunofluorescence analysis of Ki-67 expression and localisation in asynchronous
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individual human fibroblasts at different cell cycle phases defined using cell cycle markers
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cyclin D1, cyclin E1 and cyclin B1.
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B. Left: Graphs showing Ki-67 immunofluroescence staining intensity at different cell cycle
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stages in asynchronous individual cells, in HDF, U2OS and HCT-116 cells. Pixel intensity
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was quantified using ImageJ software. The legend shows the criteria for attributing cell
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cycle phases A-F (Sen: Senescent). Error bars show standard deviation. 50 cells were
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analysed in each case. Right: Example source data for quantification of cell cycle
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regulation of Ki-67 expression in asynchronous cells, showing a panel of HDF. Top:
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Hoechst staining. Cells quantified are indicated by red lables corresponding to the cell
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cycle position, according to the legend, Top left. Middle: Cyclin A immunofluorescence;
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Bottom: Ki-67 immunofluorescence.
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Supplementary Figure S4. Cell cycle arrest by serum starvation or DNA damage is
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complete.
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Analysis of DNA replication by incorporation of EdU following 72 hours of the indicated
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treatments; cells were labelled with EdU for 24 hours. Gate shows percentage of cells
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showing any level of incorporation of EdU.
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Supplementary Figure S5.
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Time course of senescence induction by bleomycin, as assessed by beta-galactosidase
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assay. Bar, 10μm
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Supplementary Figure S6.
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(A) Correlation between drug response and Ki-67, CCNA2, CCNB2, CCND1, and CCND3
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expression across all CCLE cell lines and drugs; smoothing was applied. Number is the
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correlation coefficient between expression of each gene and drug sensitivity.
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(B) Same as (A) but restricted to Irinotecan; no smoothing.
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(C) Same as (A) but restricted to Topotecan; no smoothing.
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