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

Figure 1

Overview of data, flowchart, and summary of the dynamic PPI networks in the differentiation process from hESCs to DA neurons. (a) The upper part of the timeline shows three experimental conditions (LSB: ▲, LSB/S/F8: ■, and LSB/S/F8/CHIR: ●) used in [5]. The numbers on the timeline indicates the sampling time points of microarray data (days 0, 1, 3, 5, 7, 11, and 13). The lower part of the timeline shows the three differentiation stages comprising of the data from the three experimental conditions. (b) A brief flowchart of dynamic network construction. Using PPI candidates from databases, the data of the three differentiation stages, and dynamic network modeling, three PPI networks corresponding to three differentiation stages are constructed. Then the interaction difference network (IDN) can be derived from the two networks of differentiation stages. (c) In the table at left, it shows the total number of nodes and edges at three stages. The Venn diagram at top-right shows the distribution of number of nodes between stage I and stage II and between stage II and stage III. The Venn diagram at lower right shows the distribution of number of edges between stage I (black) and stage II (red) and between stage II (black) and stage III (red).

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