Exploring the Key Genes and Pathways in the Formation of Corneal Scar Using Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32016117", "kind": "science-record", "revision": 7, "content_hash": "sha256:478d8d3b7fd88c973f1e8288fea2b31954d9dd29f16864c6c4cdc91006b2e1c6", "created_at": "2026-11-01T15:40:55Z", "updated_at": "2026-11-01T22:01:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the Key Genes and Pathways in the Formation of Corneal Scar Using Bioinformatics Analysis.", "doi": "10.1155/2020/6247489", "pmid": "32016117", "authors": ["Binfeng Liu", "Ang Li", "Hongbo Wang", "Jialin Wang", "Gongwei Zhai", "Haohao Ma", "Shiqing Feng", "Liyun Liu", "Yanzheng Gao"], "journal": "BioMed research international", "year": 2020, "abstract": "The Corneal wound healing results in the formation of opaque corneal scar. In fact, millions of people around the world suffer from corneal scars, leading to loss of vision. This study aimed to identify the key changes of gene expression in the formation of opaque corneal scar and provided potential biomarker candidates for clinical treatment and drug target discovery. We downloaded Gene expression dataset GSE6676 from NCBI-GEO, and analyzed the Differentially Expressed Genes (DEGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analyses, and protein-protein interaction (PPI) network. A total of 1377 differentially expressed genes were identified and the result of Functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) identification and protein-protein interaction (PPI) networks were performed. In total, 7 hub genes IL6 (interleukin-6), MMP9 (matrix metallopeptidase 9), CXCL10 (C-X-C motif chemokine ligand 10), MAPK8 (mitogen-activated protein kinase 8), TLR4 (toll-like receptor 4), HGF (hepatocyte growth factor), EDN1 (endothelin 1) were selected. In conclusion, the DEGS, Hub genes and signal pathways identified in this study can help us understand the molecular mechanism of corneal scar formation and provide candidate targets for the diagnosis and treatment of corneal scar.", "claims": [{"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32016117", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:32016117"], "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:GSE6676"], "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:GSE6676"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32016117", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/6247489", "sha256": "sha256:5c29891c167e35d9edf85ff2031feb5d05c4f06ea9232c8a91f88ab2b2223767", "bytes": 42200, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/6247489", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6994212", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE6676", "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=GSE6676", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6676", "version": null, "note": "All data generated or analyzed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM154328", "GSM154329", "GSM154330", "GSM154331", "GSM154332", "GSM154333", "GSM154334", "GSM154335"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Comparison of corneas from wildtype mice to those from mice under the influence of high doses of TGF-beta russe-affy-mouse-372894", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32016117:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:61306ae4a1b8fbf3c53b236ac4a5ac0f626cc8fd45e75b29cb12f0a6b4b0c35f", "bytes": 1578, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab1", "version": null, "note": "The top 10 Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched for the genes involved in module 2.", "structure": {"pmcid": "PMC6994212", "section_index": 12, "section_title": "3.4. Construction of PPI Network and Module Analysis", "row_count": 13, "column_count": 4}, "table": {"label": "Table 1", "caption": "The top 10 Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched for the genes involved in module 2.", "rows": [["Description", "P Value", "Count", "Gene symbol"], ["GO:0007186 G-protein coupled receptor protein signaling pathway (BP)", "1.25E-07", "11", "GRM5, LTB4R1, CYSLTR1, TACR3, EDN1, OXTR, PROKR1, GPR143, NMBR, HTR2B, OPN4"], ["GO:0007166 cell surface receptor linked signal transduction (BP)", "1.97E-06", "11", "GRM5, LTB4R1, CYSLTR1, TACR3, EDN1, OXTR, PROKR1, GPR143, NMBR, HTR2B, OPN4"], ["GO:0008528 peptide receptor activity, G-protein coupled (MF)", "6.35E-05", "4", "TACR3, OXTR, PROKR1, NMBR"], ["GO:0042277 peptide binding (MF)", "1.93E-04", "4", "TACR3, OXTR, PROKR1, NMBR"], ["GO:0008188 neuropeptide receptor activity (MF)", "3.53E-04", "3", "TACR3, PROKR1, NMBR"], ["GO:0042165 neurotransmitter binding (MF)", "0.001843", "3", "TACR3, PROKR1, NMBR"], ["GO:0004974 leukotriene receptor activity (MF)", "0.003007", "2", "LTB4R1, CYSLTR1"], ["GO:0003013 circulatory system process (BP)", "0.004138", "3", "EDN3, EDN1, OXTR"], ["GO:0005886 plasma membrane (CC)", "0.009375", "8", "GRM5, LTB4R1, CYSLTR1, TACR3, OXTR, PROKR1, NMBR, HTR2B"], ["GO:0042310 vasoconstriction (BP)", "0.011425", "2", "EDN3, EDN1"], ["mmu04080: Neuroactive ligand-receptor interaction", "5.51E-08", "7", "GRM5, LTB4R1, CYSLTR1, TACR3, OXTR, NMBR, HTR2B"], ["mmu04020: Calcium signaling pathway", "3.85E-05", "5", "GRM5, CYSLTR1, TACR3, OXTR, HTR2B"]], "row_count": 13, "column_count": 4, "numeric_cells": 38, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:32016117:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0245acd0880fe4babba5e72b586877e12d77d9c35073e291bb159b88596515c2", "bytes": 817, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab2", "version": null, "note": "The top 15 hub genes rank in cytoHubba.", "structure": {"pmcid": "PMC6994212", "section_index": 13, "section_title": "3.5. Hub Gene Selection", "row_count": 16, "column_count": 5}, "table": {"label": "Table 2", "caption": "The top 15 hub genes rank in cytoHubba.", "rows": [["Degree", "Stress", "MNC", "Radiality", "Closeness"], ["IL6", "IL6", "IL6", "IL6", "IL6"], ["GNGT1", "UBC", "CXCL1", "MAPK8", "MAPK8"], ["CXCL10", "MAPK8", "CXCL10", "TLR4", "TLR4"], ["TLR4", "TLR4", "GNGT1", "INS2", "MMP9"], ["CXCL1", "GNGT1", "MMP9", "HGF", "CXCL10"], ["MMP9", "POMC", "CXCL2", "MMP9", "INS2"], ["MAPK8", "INS2", "TLR4", "POMC", "POMC"], ["CXCL2", "SLCLA2", "CCR5", "CXCL10", "HGF"], ["CCR5", "HGF", "MAPK8", "EDN1", "CXCL1"], ["UBC", "SYP", "CCL20", "SLCLA2", "EDN1"], ["POMC", "CXCL10", "CXCL5", "CXCL1", "CXCL2"], ["CCL20", "PVALB", "EDN1", "UBC", "CCR5"], ["CXCL5", "EDN1", "HGF", "CCR5", "UBC"], ["HGF", "RAB3A", "CXCL3", "CCL20", "CCL20"], ["EDN1", "MMP9", "CCR3", "SYP", "GNGT1"]], "row_count": 16, "column_count": 5, "numeric_cells": 9, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tab2"}}], "gaps": ["asset:data:geo:GSE6676 not downloaded", "asset:data:geo:GSE6676 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO Enrichment"}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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