Fig. 5: C-G2P maps tumour ecosystems comprising hundreds of coexisting cancer clones. | Nature Biomedical Engineering

Fig. 5: C-G2P maps tumour ecosystems comprising hundreds of coexisting cancer clones.

From: Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships

Fig. 5

a, The tumour ecosystem. Spatial maps of tumour-intrinsic phenotypes (top) and TME phenotypes (bottom) across six topographically separated regions. Colour shade depicts aggregated log(1p)-transformed expression of phenotype-associated transcripts (colour-code as in b and d). Nodule borders are highlighted (grey). The aggregated values for all samples and underlying quantitative data of individual transcript expression can be explored through the interactive web browser interface (https://chocolat-g2p.dkfz.de/). b, Co-clustering of tumour-intrinsic phenotypes by associated transcripts. Tumour phenotypes are colour-coded. c, Associations between tumour-intrinsic and TME phenotypes. Pearson’s correlation coefficient for each pair of tumour-intrinsic and TME phenotype-associated transcripts across all nodules. d, Co-clustering of TME phenotypes by associated transcripts. TME phenotypes are colour-coded. b,d, Clustering based on Spearman correlations. Phenotypes are subdivided using hierarchical clustering. Scaled (p10) estimated plasmid probabilities per nodule are indicated (b(bottom) and d(left) (Methods). Data are derived from 324 nodules across six topographically separated regions used for 10X Visium from a single RUBIX experiment with two animals.

Back to article page