Fig. 2: Transcriptomic landscape in clusters B and C retinoblastomas (including RB1-proficient retinoblastoma).

a Volcano plot of differentially expressed transcripts between cluster A and cluster B|C. Up- and downregulated transcripts are plotted in violet and green, respectively. Key transcripts are plotted with the corresponding annotated gene symbols (Supplementary Data 6). b Box plots showing distribution of expression scores from genes representative of photoreceptor-poor, undifferentiated retinoblastoma (Liu score¹²: 3105 genes positively expressed; 3088 genes downregulated, adjusted p ≤ 0.05; or Kooi-score¹³: 3425 genes upregulated; 3477 genes downregulated, adjusted p ≤ 0.05) in 52 retinoblastomas. c Box plots showing aggregated log1p-transformed transcript tpm (transcripts per kilobase million) values and combined Storey-Tibshirani-adjusted p for MYCN and NKX2-5 expression (left) and associated gene sets (right) in 52 retinoblastomas. d Expression of transcription factors correlating with NKX2-5 and MYCN is illustrated in the circle plot. Color and size of the circles represent the correlation coefficients. e Schemes showing expression of genes defined for cluster B and C gene signatures. The top 15 upregulated and downregulated genes within these signatures are listed with the corresponding cytobands (complete outputs, Supplementary Data 15, 16). Genes encoding transcription factors are in bold. f Scatter plot demonstrating the differentially expression of genes from cluster B (524 transcripts, x-axis) and cluster C (117 transcripts, y-axis) signatures in 52 retinoblastomas. The average of log1p-transformed tpm values for a gene set was used as a signature score of each retinoblastoma sample. Boxes show upper and lower quantile and median. Whiskers extend from the hinge to ±1.5 times the interquartile range.