Identification of Key Genes and Pathways in Oxaliplatin-Induced Neuropathic Pain Through Bioinformatic Analysis

Figures & data

Figure 1 Bioinformatics analysis of the DRGs microarray datasets, GSE126773 and GSE38038, after nucleus pulposus (NP). (A) Volcano plot depicting the differentially expressed genes (DEGs) in GSE126773. (B) Volcano plot illustrating the DEGs in GSE38038. (C) Heatmap displaying the top 1000 DEGs in GSE126773. (D) Heatmap showcasing the top 1000 DEGs in GSE38038.

Figure 2 Venn diagram showing the overlapping DEGs between GSE126773 and GSE38038.

Figure 3 GO analysis and KEGG pathway analysis of the overlapping DEGs. (A) Enriched biological processes (BP) identified in GO analysis. (B) Cellular component (CC) terms enriched in GO analysis. (C) Molecular function (MF) terms enriched in GO analysis. (D) KEGG pathway enrichment analysis of the integrated DEGs.

Figure 4 Significant gene clustering module. (A) Six gene clustering modules are shown. (B-D) The three modules with the highest scores include a total of 16 genes.

Figure 5 Common enrichment analysis results, and KEGG pathway graph. (A) Gene Ontology enrichment analysis results are presented. (B) KEGG pathway enrichment analysis results are displayed.

Table 1 The Top 10 Hub Genes by Topological Analysis Methods of CytoHubba

MCC	MNC	Radiality	Closeness	Degree	EPC
Stat3	Stat3	Stat3	Stat3	Stat3	Stat3
Cd44	Casp3	Stat1	Fgf2	Fgf2	Casp3
Cxcr4	Jak2	Cd44	Stat1	Casp3	Cd44
Fgf2	Fgf2	Mapk14	Cd44	Mapk14	Fgf2
Icam1	Cd44	Fgf2	Mapk14	Stat1	Cxcr4
Mapk14	Mapk14	Jak2	Casp3	Cd44	Jak2
Stat1	Cxcr4	Icam1	Jak2	Jak2	Mapk14
Casp3	Icam1	Casp3	Cxcr4	Cxcr4	Icam1
Jak2	Stat1	Cxcr4	Icam1	Icam1	Stat1
II6	II6	II6	II6	II6	II6

Table 2 Details of the Hub genes

NO.	Gene Symbol	Full Name	Function
1	Mapk14	Mitogen-Activated Protein Kinase 14	Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway.
2	Icam1	Intercellular Adhesion Molecule 1	ICAM proteins are ligands for the leukocyte adhesion protein LFA-1 (integrin alpha-L/beta-2).
3	Cd44	CD44 Molecule	Cell-surface receptor that plays a role in cell-cell interactions, cell adhesion and migration, helping them to sense and respond to changes in the tissue microenvironment.
4	IL6	Interleukin 6	Cytokine with a wide variety of biological functions in immunity, tissue regeneration, and metabolism.
5	Cxcr4	C-X-C Motif Chemokine Receptor 4	Receptor for the C-X-C chemokine CXCL12/SDF-1 that transduces a signal by increasing intracellular calcium ion levels and enhancing MAPK1/MAPK3 activation.
6	Stat1	Signal Transducer And Activator Of Transcription 1	Signal transducer and transcription activator that mediates cellular responses to interferons (IFNs), cytokine KITLG/SCF and other cytokines and other growth factors.
7	Casp3	Caspase 3	Thiol protease that acts as a major effector caspase involved in the execution phase of apoptosis.
8	Fgf2	Fibroblast Growth Factor 2	Acts as a ligand for FGFR1, FGFR2, FGFR3 and FGFR4.

Figure 6 Venn diagram and co-expression network of hub genes. (A) The Venn diagram illustrates the overlapping hub genes identified by six different algorithms. (B) The co-expression network of hub genes and their associated genes was analyzed using GeneMANIA. (C) Module analysis revealed that eight genes were present in the three modules with the highest scores. (D) Expression patterns of the eight hub genes in the control and treatment groups. (E and F) Pathways associated with the hub genes.

Figure 7 Expression level of hub genes in GSE145222. (A-H) Comparison between data sets using a mean t test. P<0.05 was considered statistically significant. (I) Expression of hub genes in both the control and CCD groups.

Data Sharing Statement

The data that support the findings of this study are downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi; GEO accession: GSE38038; GSE126773).