Skip to main content
. Author manuscript; available in PMC: 2018 May 7.
Published in final edited form as: Nat Methods. 2017 Oct 9;14(11):1083–1086. doi: 10.1038/nmeth.4463

Figure 3. SCENIC overcomes tumor effects and unravels relevant cell states and GRNs in cancer.

Figure 3

(a-b) t-SNEs on the expression matrices, colored by tumor of origin. (c-d, f-g) t-SNEs on the binary activity matrix (e,h) after applying SCENIC. In d and g, cells are colored by GRN activity. (i) Immunohistochemistry (IHC) on 25 human melanomas using NFATC2, NFIB, ZEB1, and EPHA2 antibodies. The heatmap shows the percentage of cells that are positive for each marker in the given sample. On the right, a representative example of IHC for NFIB on a sentinel lymph node is shown (for additional images, see Supplementary Fig. 13). (j) Aggregation plots for MITF and STAT1 ChIP-seq signal on the predicted target regions, and as control randomly selected genomic regions with MITF/STAT motif occurrences.