Bioinformatics Analysis of Differentially Expressed Genes in Carpal Tunnel Syndrome Using RNA Sequencing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39415858", "kind": "science-record", "revision": 4, "content_hash": "sha256:b002a2fc1987b4f95e3aedd92b45cee06f1ecc9135766c50041e4a2b37ad7e78", "created_at": "2026-11-01T20:29:39Z", "updated_at": "2026-11-01T22:55:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of Differentially Expressed Genes in Carpal Tunnel Syndrome Using RNA Sequencing.", "doi": "10.18502/ijph.v53i8.16293", "pmid": "39415858", "authors": ["Maziar Oveisee", "Akram Gholipour", "Mahrokh Bagheri Moghaddam", "Mahshid Malakootian"], "journal": "Iranian journal of public health", "year": 2024, "abstract": "Background: Carpal tunnel syndrome (CTS) is a common disease resulting from the median nerve entrapment at the wrist. Although CTS (prevalence=5%-10% in the general population) is the most common neuropathy, its molecular mechanisms need elucidation. We used bioinformatics to detect genes with differential expressions in CTS and introduce the molecular regulatory noncoding RNAs and signaling pathways involved.\nMethods: The raw files of the RNA sequencing of CTS patients and controls were obtained from GEO (accession: GSE108023), and the samples were analyzed. Differentially expressed genes were isolated using DESeq2 R. Functional analyses were conducted on the signaling pathways, biological processes, molecular functions, and cellular components of the differentially expressed genes. Additionally, interactions between the most differentially expressed genes and miRNAs and lncRNAs were investigated bioinformatically.\nResults: Upregulation and downregulation were observed in 790 and 922 genes, respectively. The signaling pathway analysis identified the metabolism pathways of arachidonic acid, linoleic acid, and tyrosine as the most significant pathways in CTS. Moreover, PLA2G2D and PLA2G2A with upregulated expressions and PLA2G2F, PLA2G4F, PLA2G4D, PLA2G3, and PLA2G4E with downregulated expressions were genes from the phospholipase family playing significant roles in the pathways. Further analyses demonstrated that hsa-miR-3150b-3p targeted PLA2G2A and PLA2G4F, and RP11-573D15.8-018 lncRNA had regulatory interactions with the aforementioned genes.\nConclusion: Molecular studies on CTS will clarify the involved signaling pathways and provide critical data for biomedical research, drug development, and clinical applications.", "claims": [{"id": "claim-method", "statement": "The DESeq2 R package helped identify genes with differential expression patterns between the patient and control samples by considering 2 parameters: a log2FoldChange ≠5 and an adjusted P value <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39415858", "locator": "sections[4] \"Bioinformatics Analysis of Raw Sample Data\" paragraph 2", "quote": "The DESeq2 R package helped identify genes with differential expression patterns between the patient and control samples by considering 2 parameters: a log2FoldChange ≠5 and an adjusted P value <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability The supplementary table 1 (differentially expression genes between the CTS and the control group) and supplementary table 2 and 3 (miR-NAs probably targeted the 3′-UTR of PLA2G2A and PLA2G4F, respectively) are accessible through request to corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39415858", "locator": "sections[17] \"fn-group\" paragraph 1", "quote": "Data Availability The supplementary table 1 (differentially expression genes between the CTS and the control group) and supplementary table 2 and 3 (miR-NAs probably targeted the 3′-UTR of PLA2G2A and PLA2G4F, respectively) are accessible through request to corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Upregulation and downregulation were observed in 790 and 922 genes, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39415858", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Upregulation and downregulation were observed in 790 and 922 genes, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Upregulation and downregulation were observed in 790 and 922 genes, respectively.", "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:39415858"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE108023"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE108023"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39415858", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18502/ijph.v53i8.16293", "sha256": "sha256:9982027d16ca770e3a99ab94687b6f39ee21b6966301dbb6ff56e8753da5959b", "bytes": 21064, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18502/ijph.v53i8.16293", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11475164", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE108023", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108023", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108023", "version": null, "note": "Data Availability The supplementary table 1 (differentially expression genes between the CTS and the control group) and supplementary table 2 and 3 (miR-NAs probably targeted the 3′-UTR of PLA2G2A and PLA2G4F, respectively) are accessible through request to corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability The supplementary table 1 (differentially expression genes between the CTS and the control group) and supplementary table 2 and 3 (miR-NAs probably targeted the 3′-UTR of PLA2G2A and PLA2G4F, respectively) are accessible through request to corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2887483", "GSM2887484", "GSM2887485", "GSM2887486", "GSM2887487", "GSM2887488", "GSM2887489", "GSM2887490", "GSM2887491", "GSM2887492", "GSM2887493", "GSM2887494", "GSM2887495", "GSM2887496", "GSM2887497", "GSM2887498", "GSM2887499", "GSM2887500", "GSM2887501", "GSM2887502", "GSM2887503", "GSM2887504", "GSM2887505", "GSM2887506", "GSM2887507", "GSM2887508", "GSM2887509", "GSM2887510", "GSM2887511", "GSM2887512", "GSM2887513", "GSM2887514", "GSM2887515", "GSM2887516", "GSM2887517", "GSM2887518", "GSM2887519", "GSM2887520", "GSM2887521", "GSM2887522", "GSM2887523", "GSM2887524", "GSM2887525", "GSM2887526", "GSM2887527", "GSM2887528", "GSM2887529"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Genome-wide association analysis identifies 13 novel susceptibility loci for Carpal Tunnel Syndrome", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE108023 not downloaded", "asset:data:geo:GSE108023 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DESeq2 R package helped identify genes with differential expression patterns between the patient and control samples by considering 2 parameters: a log2FoldChange ≠5 and an adjusted P value <0.05."}}, {"id": "method-2", "family": "sequence_alignment", "specific": "read_mapping", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "HISAT2"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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