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. Author manuscript; available in PMC: 2019 Apr 5.
Published in final edited form as: Cell. 2018 Apr 5;173(2):291–304.e6. doi: 10.1016/j.cell.2018.03.022

Figure 4. The iCluster TumorMap.

Figure 4

(A–F) The map layout was computed from sample Euclidean similarity in the iCluster latent space, and similar samples are positioned in close proximity to each other. Each spot represents a single sample and is colored to represent attributes as described for each panel including (A) iCluster, (B) disease type, and (C) organ system. Organ systems highlighted include pan-kidney, red; pan-gyn, orange; pan-GI, blue; pan-squamous, purple; and those that overlap pan-gyn and pan-squamous, light purple.

(D) Subtypes from the pan-kidney analysis (Ricketts et al., 2018). Clear cell renal cell carcinoma (ccRCC), green; papillary renal cell carcinoma type 1 (PRCC T1), blue; papillary renal cell carcinoma type 2(PRCC T2), yellow; unclassified papillary renal cell carcinoma (PRCC Unc.), dark gray; CpG island methylator phenotype renal cell carcinoma (RCC-CIMP), red; and chromophobe renal cell carcinoma (ChRCC), purple.

(E) Subtypes from the pan-gyn group (Berger et al., 2018). Not hypermutated, with low copy-number changes (non-HM CNV low), red; hypermutated, with low copy-number changes (HM), blue; high levels of leukocyte infiltration (immune), green; low AR or PR expression (AR/PR low), orange; and high androgen receptor (AR) or progesterone receptor (PR) expression (AR/PR high), dark gray.

(F) Subtypes from the pan-GI group (Liu et al., 2018). High Epstein-Barr virus (EBV) burden, red; microsatellite instability (MSI), blue; hypermutated without MSI (HM-SNV), gold; chromosomal instability tumors (CIN), purple; and genome stable (GS) with low aneuploidy, green. The gray dots represent non-highlighted diseases.