Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation

Figure 2

The interaction activity variations of well-known proteins OTX2, FOXA2, and LMX1A in the IDNs at two differentiation stage transitions. (a) Interaction activity variation of OTX2 from LSB to LSB/S/F8; (b) of OTX2 from LSB/S/F8 to LSB/S/F8/CHIR; (c) of FOXA2 from LSB to LSB/S/F8; (d) of FOXA2 from LSB/S/F8 to LSB/S/F8/CHIR; (e) of LMX1A from LSB to LSB/S/F8; (f) of LMX1A from LSB/S/F8 to LSB/S/F8/CHIR. (Nodes: red indicates disappearance at the previous stage and appearance at the later stage. Blue indicates appearance at the previous stage and disappearance at the later stage. Purple indicates appearance under both conditions. Edges: red indicates an enhancing interaction (i.e., + → ++, − − → −, 0 → +, and − → 0). Blue indicates an attenuating interaction (++ → +, − → − −, + → 0, and 0 → −). A solid edge represents appearance under both conditions. A dashed edge represents disappearance under the previous condition and appearance under the later condition. A dotted edge represents appearance under the previous condition and disappearance under the later condition. The width of the edge represents the magnitude of the interaction activity variations.)

(a) OTX2,  LSB → LSB/S/F8

(b) OTX2, LSB/S/F8 → LSB/S/F8/CHIR

(c) FOXA2, LSB → LSB/S/F8

(d) FOXA2, LSB/S/F8 → LSB/S/F8/CHIR

(e) LMX1A, LSB → LSB/S/F8

(f) LMX1A, LSB/S/F8 → LSB/S/F8/CHIR