Fig 1.
DEGs analysis for the GSE120103 dataset.
(A) Box plot of the expression data before and (B after normalization. (C) Volcano plot of DEG between FE and FC groups. (D) Volcano plot of DEG between IE and IC groups. (E) The Venn diagram of the overlapping up-regulated DEGs in FE and IE. (F) The Venn diagram of the overlapping down-regulated DEGs in FE and IE.
Fig 2.
The lollipop charts of the 10 most significant functional enrichment analyses of GO for shared DEGs between the FE and IE groups.
(A) BP corresponding to common up-regulated DEGs, (B) MF corresponding to common up-regulated DEGs, (C) CC corresponding to common up-regulated DEGs, (D) BP corresponding to common down-regulated DEGs, (E) MF corresponding to common down-regulated DEGs, (F) CC corresponding to common down-regulated DEGs.
Fig 3.
The PPI network comprising shared up-regulated DEGs in the FE and IE groups.
The network comprises 614 nodes and 236 edges. Each node signifies a protein, while each edge denotes a protein-protein association.
Fig 4.
The top 10 genes identified using the five approaches given by the Cytoscape’s CytoHubba plugin(A) The top 10 genes identified using Betweenness method.
(B) The top 10 genes identified using BottleNeck method. (C) The top 10 genes identified using Closeness method. (D) The top 10 genes identified using Degree method. (E) The top 10 genes identified using Stress method. The colors represent high (red) to low (yellow) scores.
Fig 5.
The Venn diagram reveals the presence of two common hub genes, IL-6 and KDR, resulting from the intersection of the top 10 genes identified using the five approaches given by the Cytoscape’s CytoHubba plugin.
Fig 6.
The miRNAs/TFs-hub genes network.
The red circle, green diamond, and purple circle indicate hub genes, miRNAs, and TFs, respectively.
Table 1.
Results of the evaluation of the druggability potential of hub genes and their related TFs.
Table 2.
A list of FDA-approved drugs targeting human VEGFR2, with their binding affinity values (kcal/mol) against human VEGFR2.
Fig 7.
The binding conformation of LIF and ponatinib within the binding pocket of human VEGFR2.
(A) 3D interactions of LIF (red) and ponatinib (blue) with human VEGFR2 (tan). (B) Interactions map of LIF with human VEGFR2. (C) Interactions map of ponatinib with human VEGFR2.
Fig 8.
A graphical representation of the MD simulation results.
(A) RMSD plot. (B) RMSF plot. (C) Rg plot. (D) SASA plot.
Table 3.
Binding free energy value for VEGFR2-LIF and VEGFR2-ponatinib complexes.