Fig. 4: Oncogenic transformation and cell state.

We project the expression profiles (left, poly-A long RNA-seq), proximal network (second from right, CTCF ChIP-seq), and distal network (right, candidate cis-regulatory elements) of the ENCODE cell types to a lower dimension space. Stem-like cell types formed a cluster, suggesting stem-like cell types have a distinct profile from normal and cancerous cell types. Further, we find that cancerous cell types tend to locate closer to stem-like clusters. Oncogene knockdown in K562 led to more transcriptomic similarity to a normal cell-type, and tumor suppressor gene (TSG) knockdown led to greater similarity to a tumor cell-type (second from left, top, in comparison to GM12878). In general, we find that oncogene knockdown leads to a slight reversion towards normal state along the stem-like component (second from left, bottom).