Identification of Potential Inflammation-Related Genes and Key Pathways Associated with Complex Regional Pain Syndrome
Abstract
:1. Introduction
2. Materials and Methods
2.1. Microarray Datasets of CRPS
2.2. Differential Expression Analysis
2.3. Gene Ontology and Pathway Enrichment Analysis
2.4. Protein–Protein Interaction (PPI) Network Analysis
2.5. Gene Set Enrichment Analyses (GSEA)
2.6. Establishment of Predictive Models
2.7. Ethical Declaration
3. Results
3.1. Identification of CRPS-Associated Genes
3.2. Functional Annotation
3.3. PPI Network Analysis and GSEA Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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ID | Gene Symbol | p Value | Log Fc | Gene Title |
---|---|---|---|---|
ILMN_1715169 | HLA-DRB1 | 4.06 × 10−10 | 3.90 | Major histocompatibility complex, class II, DR beta 1 |
ILMN_1670130 | ARID3A | 2.17 × 10−7 | 3.71 | AT-rich interaction domain 3A |
ILMN_1738075 | CMIP | 2.14 × 10−6 | 1.65 | c-Maf inducing protein |
ILMN_1696643 | TLN1 | 2.14 × 10−6 | 1.63 | Talin 1 |
ILMN_2371169 | ZYX | 2.42 × 10−6 | 1.50 | Zyxin |
ILMN_1722872 | MYH9 | 3.71 × 10−6 | 1.47 | Myosin, heavy chain 9, non-muscle |
ILMN_1782385 | POLR2A | 5.04 × 10−6 | 1.45 | RNA polymerase II subunit A |
ILMN_1728724 | IL17RA | 5.91 × 10−6 | 1.42 | Interleukin 17 receptor A |
ILMN_1790689 | CRISPLD2 | 1.19 × 10−5 | 1.37 | Cysteine rich secretory protein LCCL domain containing 2 |
ILMN_1701875 | ZYX | 1.24 × 10−5 | 1.33 | Zyxin |
ILMN_1694810 | PANX2 | 1.39 × 10−5 | 1.31 | Pannexin 2 |
ILMN_3241091 | TM × 10M164 | 2.38 × 10−5 | 1.30 | Transmembrane protein 164 |
ILMN_1793729 | C15orf39 | 3.11 × 10−5 | 1.28 | Chromosome 15 open reading frame 39 |
ILMN_1763837 | ANPEP | 3.54 × 10−5 | 1.25 | Alanyl aminopeptidase, membrane |
ILMN_1665964 | GAB2 | 4.09 × 10−5 | 1.24 | GRB2 associated binding protein 2 |
ILMN_1711838 | SLC25A24 | 9.17 × 10−5 | 1.23 | Solute carrier family 25 member 24 |
ILMN_1717207 | MMP25 | 1.01 × 10−4 | 1.22 | Matrix metallopeptidase 25 |
ILMN_2232177 | ACTN1 | 1.75 × 10−4 | 1.20 | Actinin alpha 1 |
ILMN_1661266 | HLA-DQB1 | 1.97 × 10−4 | 1.19 | Major histocompatibility complex, class II, DQ beta 1 |
ILMN_2371280 | CSF3R | 3.06 × 10−4 | 1.18 | Colony stimulating factor 3 receptor |
ILMN_2356991 | CD47 | 3.56 × 10−4 | 1.18 | CD47 molecule |
ILMN_1736190 | CYP4F3 | 5.75 × 10−4 | 1.17 | Cytochrome P450 family 4 subfamily F member 3 |
ILMN_1677511 | PTGS2 | 8.13 × 10−4 | 1.17 | Prostaglandin-endoperoxide synthase 2 |
ILMN_2184373 | CXCL8 | 8.98 × 10−4 | 1.13 | C-X-C motif chemokine ligand 8 |
ILMN_1792323 | HDC | 1.01 × 10−3 | 1.11 | Histidine decarboxylase |
ILMN_2054297 | PTGS2 | 1.25 × 10−3 | 1.10 | Prostaglandin-endoperoxide synthase 2 |
ILMN_1666733 | CXCL8 | 1.43 × 10−3 | 1.10 | C-X-C motif chemokine ligand 8 |
ILMN_1810420 | DYSF | 1.90 × 10−3 | 1.10 | Dysferlin |
ILMN_3242315 | SNORD3D | 1.98 × 10−3 | 1.08 | Small nucleolar RNA, C/D box 3D |
ILMN_1747935 | GOLGB1 | 2.49 × 10−3 | 1.08 | Olgin B1 |
ILMN_1780546 | OSM | 3.28 × 10−3 | 1.06 | Oncostatin M |
ILMN_1796316 | MMP9 | 5.24 × 10−3 | 1.02 | Matrix metallopeptidase 9 |
ILMN_1723116 | AMFR | 8.38 × 10−3 | 1.01 | Autocrine motility factor receptor |
ILMN_1745522 | PF4V1 | 1.00 × 10−2 | −1.04 | Platelet factor 4 variant 1 |
ILMN_2165753 | HLA-A | 1.18 × 10−2 | −1.29 | Major histocompatibility complex, class I, A |
ILMN_1705458 | TRIM58 | 3.08 × 10−2 | −1.31 | Tripartite motif containing 58 |
ILMN_2132809 | ARHGEF10 | 3.88 × 10−2 | −2.47 | Rho guanine nucleotide exchange factor 10 |
GO ID | Term | Count | p Value | Fold Enrichment |
---|---|---|---|---|
BP | ||||
GO:0002504 | Antigen processing | 3 | 0.0005 | 90.5 |
GO:0050870 | Positive regulation of T cell activation | 3 | 0.0013 | 54.9 |
GO:0019882 | Antigen processing and presentation | 3 | 0.0026 | 38.5 |
GO:0007229 | Integrin-mediated signaling pathway | 4 | 0.0007 | 21.9 |
GO:0006954 | Inflammatory response | 5 | 0.0041 | 7.3 |
CC | ||||
GO:0042613 | MHC class II protein complex | 3 | 0.0008 | 69.8 |
GO:0071556 | Reticulum membrane | 3 | 0.0010 | 62.6 |
GO:0012507 | Golgi transport vesicle membrane | 3 | 0.0038 | 31.8 |
GO:0030666 | Endocytic vesicle membrane | 3 | 0.0058 | 25.6 |
GO:0005765 | Lysosomal membrane | 5 | 0.0030 | 8.0 |
MF | ||||
GO:0042605 | Peptide antigen binding | 3 | 0.0016 | 49.4 |
GO:0005178 | Integrin binding | 3 | 0.0269 | 11.3 |
GO:0051015 | Actin filament binding | 3 | 0.0499 | 8.1 |
KEGG Pathway ID | Term | Count | p Value | Fold Enrichment |
---|---|---|---|---|
hsa05330 | Allograft rejection | 3 | 0.0042 | 29.3 |
hsa05332 | Graft-versus-host disease | 3 | 0.0051 | 26.5 |
hsa04940 | Type I diabetes mellitus | 3 | 0.0053 | 25.9 |
hsa05320 | Autoimmune thyroid disease | 3 | 0.0080 | 21.0 |
hsa05416 | Viral myocarditis | 3 | 0.0102 | 18.6 |
hsa04640 | Hematopoietic cell lineage | 4 | 0.0020 | 15.0 |
hsa04612 | Antigen processing and presentation | 3 | 0.0168 | 14.3 |
hsa05323 | Rheumatoid arthritis | 3 | 0.0234 | 12.0 |
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Zhu, H.; Wen, B.; Xu, L.; Huang, Y. Identification of Potential Inflammation-Related Genes and Key Pathways Associated with Complex Regional Pain Syndrome. Biomolecules 2023, 13, 772. https://doi.org/10.3390/biom13050772
Zhu H, Wen B, Xu L, Huang Y. Identification of Potential Inflammation-Related Genes and Key Pathways Associated with Complex Regional Pain Syndrome. Biomolecules. 2023; 13(5):772. https://doi.org/10.3390/biom13050772
Chicago/Turabian StyleZhu, He, Bei Wen, Li Xu, and Yuguang Huang. 2023. "Identification of Potential Inflammation-Related Genes and Key Pathways Associated with Complex Regional Pain Syndrome" Biomolecules 13, no. 5: 772. https://doi.org/10.3390/biom13050772