Table 1 Top 5 densely connected modules in the protein–protein interaction network, with enrichment analysis results

From: An integrated proteomics and metabolomics analysis of methylglyoxal-induced neurotoxicity in a human neuroblastoma cell line

Module

Node

Edge

Enriched term

FDR

Protein (gene name)

Module 1

32

459

Ribosome biogenesis in eukaryotes (hsa03008)

1.4 × 10−12

RBM28↑, TBL3↑, UTP4↑, NOB1↓, WDR3↑, WDR75↑, PWP2↑, GTPBP4↑, GNL3↑

rRNA processing (GO:0006364)

4.8 × 10−17

DDX27↑, DDX47↑, PPAN↑, WDR75↑, BOP1↑, TBL3↑, EBNA1BP2↑, PDCD11↑, NOB1↓, PES1↑, MRTO4↑, ESF1↑, BRIX1↑

Module 2

26

186

Ribosome (hsa03010)

3.2 × 10−4

RPS26↑, RPS27↓, RPL32↓, RPS29↓, RPS12↑

Translational initiation (GO:0006413)

7.0 × 10−26

EIF4A1↑, EIF1AX↑, EIF2S1↑, EIF1↑, EIF3M↑, EIF2S3↑, EIF6↑, EIF3L↑, EIF3I↑, EIF3J↑, EIF3H↑, EIF3C↑, EIF3D↑, EIF4G1↑

Module 3

9

29

Focal adhesion (hsa04510)

7.7 × 10−10

ITGB1↓, COL1A1↓, ITGA3↓, ITGAV↓, ITGA6↓, LAMB1↓, TLN2↓, FLNC↑

ECM–receptor interaction (hsa04512)

7.8 × 10−8

ITGB1↓, COL1A1↓, ITGA3↓, ITGAV↓, ITGA6↓, LAMB1↓

Module 4

6

14

Oxidative phosphorylation (hsa00190)

1.6 × 10−9

NDUFA7↓, UQCRB↑, NDUFB4↓, NDUFS4↑, COX5B↓, ATP5F1D↑

Module 5

22

37

Nrf2 pathway (WP2884)

6.0 × 10−3

NQO1↑, TXNRD1↑, HMOX1↑, TXN↑, GCLM↑

  1. Enrichment analysis was conducted using DAVID for each module presented in Fig. 3. Representative terms were selected for each module to highlight key biological functions. Proteins were indicated by their corresponding gene names, which were retrieved from UniProt38. “↑” indicates upregulated protein expression, while “↓” signifies downregulated protein expression.
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