Figure 4
From: A physical sciences network characterization of non-tumorigenic and metastatic cells
Comparative molecular signatures for morphology, motility and stress.
(a) The largest connected subnetwork of transcription factors from the master network (Suppl. Fig. 3) with nodes colored to provide a "summary" of the entire network. Node size shows the number of edges (connecting lines) in the master network that were above a cutoff for specificity to either cell line. Larger nodes have more cell-line-specific edges; the largest, IKZF1, has 67 edges above the threshold. Node color is determined by the ratio of above-cutoff edges specific to MCF-10A vs. MDA-MB-231, with yellow denoting more MCF-10A edges and blue more MDA-MB-231 edges. Nodes with many edges specific to one cell line or the other are therefore large and brightly colored, such as IKZF1 or COPS2. (b-d) One-hop networks from transcription factor regulators (â–µ) to their targets (â—‹). Each gene is represented as a 'node'. If a gene's abundance is regulated by another gene, this is denoted with an 'edge' between those genes. Color of an edge indicates the specificity of that regulatory relationship to either MCF-10A cells (yellow) or MDA-MB-231 cells (blue). Relationships that are equally present in both cell types are demarked grey. Node border color indicates differential proteomics results. Yellow border nodes are upregulated in MCF-10A cells. Blue border nodes are upregulated in MDA-MB-231 cells. Grey bordered nodes were quantified and found to be equivalent in both cell types. (b) Morphology network. The 1-hop morphology network from FBN1 and TWIST1, LOX and LOXL1, both putatively regulated by FBN1. Both FBN1 and TWIST1 are putatively regulated by ZEB1. Also shown are the large number of MDA-MB-231 edges from FBN1 and a fairly even distribution of edges from ZEB1. (c) Motility network. The 1-hop network from ITGB4. ITGB4 is itself a gene of interest and is inferred to regulate EGFR and several laminins. (d) Stress response network. The 1-hop network from HIF1A, a transcription factor and gene of interest. It is putatively regulated by MET (upper triangle), which is also inferred to regulate ITGB4. HIF1A putatively regulates two more genes of interest, LOX (also a putative target of FBN1 and SATB2).
