A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks

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. 2019 Jan 8;10(1):31. doi: 10.3390/genes10010031

Algorithm 2 Active PPI network fusion

Input: Active networks of each time point, parameter K.

Output: Final fused network.

Step1: Construct adjacency matrix W_i of the ith active network (I = 1, 2, 3, 4, …, M) using Equation (5).

Step2: Construct P_i and S_i of the ith active network using Equations (8) and (9).

Step3: Calculate the similarities between any two networks based on the Euclidean distance of their adjacency matrixes.

Step4: Select the nearest two active networks G_i and G_j,

P_{i}^{0} = P_{i}

P_{j}^{0} = P_{j}

, t = 0.
Step5: Compute

P_{i}^{t + 1}

and

P_{j}^{t + 1}

using Equations (10) and (11), let t = t + 1.
Step6: Repeat step 5 until t = 20.
Step7: Compute the fused network R of G_i and G_j using Equation (12).
Step8: Let W_r = R, construct P_r and S_r of the fused network R using Equation (8) and (9).
Step9: Find the nearest active network G_k to R from the remaining active networks, let

P_{k}^{0}

P_{k}

, t = 0.
Step10: Compute

P_{r}^{t + 1}

and

P_{k}^{t + 1}

using Equations (10) and (11), let t = t + 1.
Step11: Repeat step 10 until t = 20.
Step12: Compute the fused network of R and G_k using Equation (12), the fused network is named as R.
Step13: Remove G_k from active network list and repeat steps 8 to 12 until all the active networks are fused to a final network.
Step14: Output the final fused network.