Fig 1.
Analysis workflow diagram with steps for (1) Data Preprocessing, (2) Building PPI Networks, (3) Generating Node Embeddings, (4) Distance Calculation, (5) Outlier Detection, (6) Enrichment Analysis.
Fig 2.
Frequency histogram showing the distribution of network edge weights after rescaling to a range of 0-2 for (A) CT2-Control, (B) CT2-lgDel.
Fig 3.
Log-scaled frequency histogram showing the distribution of Euclidean distances between protein nodes in (A) CT2-lgDel vs. CT2-Control networks and (B) CT2-Control-A vs. CT2-Control-B networks.
Fig 4.
Venn Diagrams showing overlap in candidates genes identified in (A) CT2-lgDel and H9-lgDel, (B) CT2-lgDel and CT2-smDel, (C) CT2-lgDel and Dental Pulp, (D) all four analyses.
Table 1.
CT2-lgDel functional enrichment clusters.
Table 2.
H9-lgDel functional enrichment clusters.
Fig 5.
Network showing the protein-protein interactions among the glycosylation enzymes that are CT2-lgDel and/or H9-lgDel candidates.
Nodes with black borders are CT-lgDel candidates; nodes with blue borders are H9-lgDel candidates; nodes with red borders are both CT2-lgDel and H9-lgDel candidates. Yellow node fill color indicates the protein is annotated with the following enriched GO Biological Process terms: (A) Protein O-linked glycosylation (GO:0006493; FDR for enrichment in the network = 9.57e-16); (B) Aminoglycan biosynthetic process (GO:0006023; FDR = 5.24e-13); (C) Fucosylation (GO:0036065; FDR = 3.06E-05); (D) Heparan sulfate proteoglycan metabolic process (GO:0030201; FDR = 1.6e-04).
Fig 6.
Networks showing protein-protein interactions among CT2-lgDel candidate glycosylation enzymes and their CT2-lgDel candidate first neighbors.
Nodes with black borders are glycosylation enzymes that are CT2-lgDel candidates; nodes with red borders are glycosylation enzymes that are both CT2-lgDel and H9-lgDel candidates. Node fill color indicates Euclidean distance between lgDel and control networks. The network clustered into three sub-networks centered around different subsets of glycosylation enzymes. Clusters 1-3 shown in (A)-(C), respectively.
Fig 7.
Network showing the protein-protein interactions among the proteins from the DAVID Homeobox cluster that are CT2-lgDel and/or H9-lgDel candidates.
Nodes with black borders are CT-lgDel candidates; nodes with blue borders are H9-lgDel candidates; nodes with red borders are both CT2-lgDel and H9-lgDel candidates. Node fill color indicates GO Biological Process annotations: Yellow: Nervous system development (GO:0007399; FDR for enrichment in the network = 4.34E-32; Pink: Dopaminergic neuron differentiation (GO:0071542; FDR = 1.22E-07; Purple: GABAergic neuron differentiation (GO:0097154; FDR = 4.83E-06).