Identification of candidate genes and miRNAs associated with neuropathic pain induced by spared nerve injury.

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Microarray data (access number GSE91396) were downloaded from the Gene Expression Omnibus (GEO). Murine RNA‑seq samples from three brain regions [nucleus accumbens, (NAc); medial prefrontal cortex, (mPFC) and periaqueductal gray, (PAG)]were compared between the spared nerve injury (SNI) model and a sham surgery. After data normalization, differentially expressed RNAs were screened using the limma package and functional enrichment analysis was performed with Database for Annotation, Visualization and Integrated Discovery. The microRNA (miRNA/miR)‑mRNA regulatory network and miRNA‑target gene‑pathway regulatory network were constructed using Cytoscape software. A total of 2,776 differentially expressed RNAs (219 miRNAs and 2,557 mRNAs) were identified in the SNI model compared with the sham surgery group. A total of two important modules (red and turquoise module) were found to be related to NP using weighed gene co‑expression network analysis (WGCNA) for the 2,325 common differentially expressed RNAs in three brain regions. The differentially expressed genes (DEGs) in the miRNA‑mRNA regulatory network were significantly enriched in 21 Gene Ontology terms and five pathways. A total of four important DEGs (CXCR2, IL12B, TNFSF8 and GRK1) and five miRNAs (miR‑208a‑5p, miR‑7688‑3p, miR‑344f‑3p, miR‑135b‑3p and miR‑135a‑2‑3p) were revealed according to the miRNA‑target gene‑pathway regulatory network to be related to NP. Four important DEGs (CXCR2, IL12B, TNFSF8 and GRK1) and five miRNAs (miR‑208a‑5p, miR‑7688‑3p, miR‑344f‑3p, miR‑135b‑3p and miR‑135a‑2‑3p) were differentially expressed in SNI, indicating their plausible roles in NP pathogenesis.", "claims": [{"id": "claim-method", "statement": "The WGCNA package (27) version 1.61 in R3.4.1 software (cran.r-project.org/web/packages/WGCNA/) was used to analyze the correlation with disease status for common differentially expressed RNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31432094", "locator": "sections[4] \"Analysis of the common differentially expressed RNAs for all the three brain regions\" paragraph 3", "quote": "The WGCNA package (27) version 1.61 in R3.4.1 software (cran.r-project.org/web/packages/WGCNA/) was used to analyze the correlation with disease status for common differentially expressed RNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable requests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31432094", "locator": "sections[16] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable requests."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31432094"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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