Fig. 3

Protein-protein interaction (PPI) and functional enrichment of differentially methylated genes in FCD 3D with loss of layer 4. 3a PPI networks of FCD 3D subgroups. Differentially methylated genes are marked in pink, and connector nodes are shown in blue. The loss of layer 4 subgroup showed the largest connected PPI network with four major topological modules. b They centered around HNRNPL, VIRMA, UBA52, and APP. The UBA52 module significantly overrepresented proteins involved in TNF and death receptor signaling. c Functional enrichment of the FCD 3D with loss of layer 4 PPI network highlighted neurodegeneration (KEGG), cytoskeleton organization, and nervous system and anatomical structure development (GO:BP) mainly targeting neuron projections and spine (GO:CC) as central disease mechanisms. APP - Amyloid Beta Precursor Protein, BP – Biological Process, CC – Cellular Component, Dev. – development/developmental, FCD – Focal Cortical Dysplasia, GO – Gene Ontology, HNRNPL -Heterogeneous Nuclear Ribonucleoprotein L, KEGG – Kyoto Encyclopedia of Genes and Genomes, TNF – Tumor Necrosis Factor, UBA52 - Ubiquitin A-52 Residue Ribosomal Protein Fusion, VIRMA - Vir Like M6A Methyltransferase Associated