Identification and Verification of Five Potential Biomarkers Related to Skin and Thermal Injury Using Weighted Gene Co-Expression Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35047008", "kind": "science-record", "revision": 4, "content_hash": "sha256:ef5cdd811c449641a42f34384960b061c215082d7224ef8a6b52a216076dd6a4", "created_at": "2026-11-01T17:36:46Z", "updated_at": "2026-11-01T22:05:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Verification of Five Potential Biomarkers Related to Skin and Thermal Injury Using Weighted Gene Co-Expression Network Analysis.", "doi": "10.3389/fgene.2021.781589", "pmid": "35047008", "authors": ["Ronghua Yang", "Zhengguang Wang", "Jiehua Li", "Xiaobing Pi", "Xiaoxiang Wang", "Yang Xu", "Yan Shi", "Sitong Zhou"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Background: Burn injury is a life-threatening disease that does not have ideal biomarkers. Therefore, this study first applied weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) screening methods to identify pivotal genes and diagnostic biomarkers associated with the skin burn process. Methods: After obtaining transcriptomic datasets of burn patient skin and normal skin from Gene Expression Omnibus (GEO) and performing differential analysis and functional enrichment, WGCNA was used to identify hub gene modules associated with burn skin processes in the burn patient peripheral blood sample dataset and determine the correlation between modules and clinical features. Enrichment analysis was performed to identify the functions and pathways of key module genes. Differential analysis, WGCNA, protein-protein interaction analysis, and enrichment analysis were utilized to screen for hub genes. Hub genes were validated in two other GEO datasets, tested by immunohistochemistry for hub gene expression in burn patients, and receiver operating characteristic curve analysis was performed. Finally, we constructed the specific drug activity, transcription factors, and microRNA regulatory network of the five hub genes. Results: A total of 1,373 DEGs in GSE8056 were obtained, and the top 5 upregulated genes were S100A12, CXCL8, CXCL5, MMP3, and MMP1, whereas the top 5 downregulated genes were SCGB1D2, SCGB2A2, DCD, TSPAN8, and KRT25. DEGs were significantly enriched in the immunity, epidermal development, and skin development processes. In WGCNA, the yellow module was identified as the most closely associated module with tissue damage during the burn process, and the five hub genes (ANXA3, MCEMP1, MMP9, S100A12, and TCN1) were identified as the key genes for burn injury status, which consistently showed high expression in burn patient blood samples in the GSE37069 and GSE13902 datasets. Furthermore, we verified using immunohistochemistry that these five novel hub genes were also significantly elevated in burn patient skin. In addition, MCEMP1, MMP9, and S100A12 showed perfect diagnostic performance in the receiver operating characteristic analysis. Conclusion: In conclusion, we analyzed the changes in genetic processes in the skin during burns and used them to identify five potential novel diagnostic markers in blood samples from burn patients, which are important for burn patient diagnosis. In particular, MCEMP1, MMP9, and S100A12 are three key blood biomarkers that can be used to identify skin damage in burn patients.", "claims": [{"id": "claim-method", "statement": "Weighted gene co-expression network analysis (WGCNA) (Langfelder and Horvath, 2008), a novel systems biology method, assists in the construction of free-scale gene co-expression networks and the detection of gene modules and hub genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35047008", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "Weighted gene co-expression network analysis (WGCNA) (Langfelder and Horvath, 2008), a novel systems biology method, assists in the construction of free-scale gene co-expression networks and the detection of gene modules and hub genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35047008", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We obtained 5 modules except for the gray module, in which the yellow consensus module was the most relevant module with burn traits (correlation value = 0.89; significance level p < 0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "We obtained 5 modules except for the gray module, in which the yellow consensus module was the most relevant module with burn traits (correlation value = 0.89; significance level p < 0.05)."}, "evidence": [{"asset": "source:pmid:35047008", "locator": "sections[16] \"WGCNA and Identification of Hub Genes\" paragraph 2", "quote": "We obtained 5 modules except for the gray module, in which the yellow consensus module was the most relevant module with burn traits (correlation value = 0.89; significance level p < 0.05)."}, {"asset": "source:pmid:35047008", "locator": "sections[16] \"WGCNA and Identification of Hub Genes\" paragraph 2", "quote": "Furthermore, 30 hub genes were selected in yellow co-expression modules with gene significance >0.8 and module membership >0.8."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We obtained 5 modules except for the gray module, in which the yellow consensus module was the most relevant module with burn traits (correlation value = 0.89; significance level p < 0.05).", "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:35047008"], "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:GSE123568"], "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:GSE123568"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35047008", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2021.781589", "sha256": "sha256:bc35dab1aa13c4433ce2a0bfa5077e891b0a3a2b144eddd049bc782a67c4d0e8", "bytes": 40649, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2021.781589", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8762241", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE123568", "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=GSE123568", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE123568", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3507251", "GSM3507252", "GSM3507253", "GSM3507254", "GSM3507255", "GSM3507256", "GSM3507257", "GSM3507258", "GSM3507259", "GSM3507260", "GSM3507261", "GSM3507262", "GSM3507263", "GSM3507264", "GSM3507265", "GSM3507266", "GSM3507267", "GSM3507268", "GSM3507269", "GSM3507270", "GSM3507271", "GSM3507272", "GSM3507273", "GSM3507274", "GSM3507275", "GSM3507276", "GSM3507277", "GSM3507278", "GSM3507279", "GSM3507280", "GSM3507281", "GSM3507282", "GSM3507283", "GSM3507284", "GSM3507285", "GSM3507286", "GSM3507287", "GSM3507288", "GSM3507289", "GSM3507290"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Identification of Potential Biomarkers for Improving the Precision of Early Detection of Steroid-induced Osteonecrosis of the Femoral Head", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE13902", "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=GSE13902", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13902", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM350095", "GSM350102"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "3154", "taxon": "Escherichia coli", "title": "BW25113 fhlA/pCA24N-FhlA133 vs fhlA/pCA24N-FhlA in modified-complex 20 mM formate at 37ºC", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE139028", "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=GSE139028", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE139028", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4127070", "GSM4127071", "GSM4127072", "GSM4127073", "GSM4127074", "GSM4127075", "GSM4127076", "GSM4127077", "GSM4127078"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "15433", "taxon": "Homo sapiens", "title": "RNA-seq analysis on tissues derived from normal skin and burn eschar", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE19743", "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=GSE19743", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19743", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM493655", "GSM493656", "GSM493657", "GSM493658", "GSM493659", "GSM493660", "GSM493661", "GSM493662", "GSM493663", "GSM493664", "GSM493665", "GSM493666", "GSM493667", "GSM493668", "GSM493669", "GSM493670", "GSM493671", "GSM493672", "GSM493673", "GSM493674", "GSM493675", "GSM493676", "GSM493677", "GSM493678", "GSM493679", "GSM493680", "GSM493681", "GSM493682", "GSM493683", "GSM493684", "GSM493685", "GSM493686", "GSM493687", "GSM493688", "GSM493689", "GSM493690", "GSM493691", "GSM493692", "GSM493693", "GSM493694", "GSM493695", "GSM493696", "GSM493697", "GSM493698", "GSM493699", "GSM493700", "GSM493701", "GSM493702", "GSM493703", "GSM493704", "GSM493705", "GSM493706", "GSM493707", "GSM493708", "GSM493709", "GSM493710", "GSM493711", "GSM493712", "GSM493713", "GSM493714", "GSM493715", "GSM493716", "GSM493717", "GSM493718", "GSM493719", "GSM493720", "GSM493721", "GSM493722", "GSM493723", "GSM493724", "GSM493725", "GSM493726", "GSM493727", "GSM493728", "GSM493729", "GSM493730", "GSM493731", "GSM493732", "GSM493733", "GSM493734", "GSM493735", "GSM493736", "GSM493737", "GSM493738", "GSM493739", "GSM493740", "GSM493741", "GSM493742", "GSM493743", "GSM493744", "GSM493745", "GSM493746", "GSM493747", "GSM493748", "GSM493749", "GSM493750", "GSM493751", "GSM493752", "GSM493753", "GSM493754", "GSM493755", "GSM493756", "GSM493757", "GSM493758", "GSM493759", "GSM493760", "GSM493761", "GSM493762", "GSM493763", "GSM493764", "GSM493765", "GSM493766", "GSM493767", "GSM493768", "GSM493769", "GSM493770", "GSM493771", "GSM493772", "GSM493773", "GSM493774", "GSM493775", "GSM493776", "GSM493777", "GSM493778", "GSM493779", "GSM493780", "GSM493781", "GSM493782", "GSM493783", "GSM493784", "GSM493785", "GSM493786", "GSM493787", "GSM493788", "GSM493789", "GSM493790", "GSM493791", "GSM493792", "GSM493793", "GSM493794", "GSM493795", "GSM493796", "GSM493797", "GSM493798", "GSM493799", "GSM493800", "GSM493801", "GSM493802", "GSM493803", "GSM493804", "GSM493805", "GSM493806", "GSM493807", "GSM493808", "GSM493809", "GSM493810", "GSM493811", "GSM493812", "GSM493813", "GSM493814", "GSM493815", "GSM493816", "GSM493817", "GSM493818", "GSM493819", "GSM493820", "GSM493821", "GSM493822", "GSM493823", "GSM493824", "GSM493825", "GSM493826", "GSM493827", "GSM493828", "GSM493829", "GSM493830", "GSM493831"], "sample_count": 177, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A large-scale clinical study of gene expression response to severe burn injury", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37069", "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=GSE37069", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37069", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM909644", "GSM909645", "GSM909646", "GSM909647", "GSM909648", "GSM909649", "GSM909650", "GSM909651", "GSM909652", "GSM909653", "GSM909654", "GSM909655", "GSM909656", "GSM909657", "GSM909658", "GSM909659", "GSM909660", "GSM909661", "GSM909662", "GSM909663", "GSM909664", "GSM909665", "GSM909666", "GSM909667", "GSM909668", "GSM909669", "GSM909670", "GSM909671", "GSM909672", "GSM909673", "GSM909674", "GSM909675", "GSM909676", "GSM909677", "GSM909678", "GSM909679", "GSM909680", "GSM909681", "GSM909682", "GSM909683", "GSM909684", "GSM909685", "GSM909686", "GSM909687", "GSM909688", "GSM909689", "GSM909690", "GSM909691", "GSM909692", "GSM909693", "GSM909694", "GSM909695", "GSM909696", "GSM909697", "GSM909698", "GSM909699", "GSM909700", "GSM909701", "GSM909702", "GSM909703", "GSM909704", "GSM909705", "GSM909706", "GSM909707", "GSM909708", "GSM909709", "GSM909710", "GSM909711", "GSM909712", "GSM909713", "GSM909714", "GSM909715", "GSM909716", "GSM909717", "GSM909718", "GSM909719", "GSM909720", "GSM909721", "GSM909722", "GSM909723", "GSM909724", "GSM909725", "GSM909726", "GSM909727", "GSM909728", "GSM909729", "GSM909730", "GSM909731", "GSM909732", "GSM909733", "GSM909734", "GSM909735", "GSM909736", "GSM909737", "GSM909738", "GSM909739", "GSM909740", "GSM909741", "GSM909742", "GSM909743", "GSM909744", "GSM909745", "GSM909746", "GSM909747", "GSM909748", "GSM909749", "GSM909750", "GSM909751", "GSM909752", "GSM909753", "GSM909754", "GSM909755", "GSM909756", "GSM909757", "GSM909758", "GSM909759", "GSM909760", "GSM909761", "GSM909762", "GSM909763", "GSM909764", "GSM909765", "GSM909766", "GSM909767", "GSM909768", "GSM909769", "GSM909770", "GSM909771", "GSM909772", "GSM909773", "GSM909774", "GSM909775", "GSM909776", "GSM909777", "GSM909778", "GSM909779", "GSM909780", "GSM909781", "GSM909782", "GSM909783", "GSM909784", "GSM909785", "GSM909786", "GSM909787", "GSM909788", "GSM909789", "GSM909790", "GSM909791", "GSM909792", "GSM909793", "GSM909794", "GSM909795", "GSM909796", "GSM909797", "GSM909798", "GSM909799", "GSM909800", "GSM909801", "GSM909802", "GSM909803", "GSM909804", "GSM909805", "GSM909806", "GSM909807", "GSM909808", "GSM909809", "GSM909810", "GSM909811", "GSM909812", "GSM909813", "GSM909814", "GSM909815", "GSM909816", "GSM909817", "GSM909818", "GSM909819", "GSM909820", "GSM909821", "GSM909822", "GSM909823", "GSM909824", "GSM909825", "GSM909826", "GSM909827", "GSM909828", "GSM909829", "GSM909830", "GSM909831", "GSM909832", "GSM909833", "GSM909834", "GSM909835", "GSM909836", "GSM909837", "GSM909838", "GSM909839", "GSM909840", "GSM909841", "GSM909842", "GSM909843", "GSM909844", "GSM909845", "GSM909846", "GSM909847", "GSM909848", "GSM909849", "GSM909850", "GSM909851", "GSM909852", "GSM909853", "GSM909854", "GSM909855", "GSM909856", "GSM909857", "GSM909858", "GSM909859", "GSM909860", "GSM909861", "GSM909862", "GSM909863", "GSM909864", "GSM909865", "GSM909866", "GSM909867", "GSM909868", "GSM909869", "GSM909870", "GSM909871", "GSM909872", "GSM909873", "GSM909874", "GSM909875", "GSM909876", "GSM909877", "GSM909878", "GSM909879", "GSM909880", "GSM909881", "GSM909882", "GSM909883", "GSM909884", "GSM909885", "GSM909886", "GSM909887", "GSM909888", "GSM909889", "GSM909890", "GSM909891", "GSM909892", "GSM909893", "GSM909894", "GSM909895", "GSM909896", "GSM909897", "GSM909898", "GSM909899", "GSM909900", "GSM909901", "GSM909902", "GSM909903", "GSM909904", "GSM909905", "GSM909906", "GSM909907", "GSM909908", "GSM909909", "GSM909910", "GSM909911", "GSM909912", "GSM909913", "GSM909914", "GSM909915", "GSM909916", "GSM909917", "GSM909918", "GSM909919", "GSM909920", "GSM909921", "GSM909922", "GSM909923", "GSM909924", "GSM909925", "GSM909926", "GSM909927", "GSM909928", "GSM909929", "GSM909930", "GSM909931", "GSM909932", "GSM909933", "GSM909934", "GSM909935", "GSM909936", "GSM909937", "GSM909938", "GSM909939", "GSM909940", "GSM909941", "GSM909942", "GSM909943", "GSM909944", "GSM909945", "GSM909946", "GSM909947", "GSM909948", "GSM909949", "GSM909950", "GSM909951", "GSM909952", "GSM909953", "GSM909954", "GSM909955", "GSM909956", "GSM909957", "GSM909958", "GSM909959", "GSM909960", "GSM909961", "GSM909962", "GSM909963", "GSM909964", "GSM909965", "GSM909966", "GSM909967", "GSM909968", "GSM909969", "GSM909970", "GSM909971", "GSM909972", "GSM909973", "GSM909974", "GSM909975", "GSM909976", "GSM909977", "GSM909978", "GSM909979", "GSM909980", "GSM909981", "GSM909982", "GSM909983", "GSM909984", "GSM909985", "GSM909986", "GSM909987", "GSM909988", "GSM909989", "GSM909990", "GSM909991", "GSM909992", "GSM909993", "GSM909994", "GSM909995", "GSM909996", "GSM909997", "GSM909998", "GSM909999", "GSM910000", "GSM910001", "GSM910002", "GSM910003", "GSM910004", "GSM910005", "GSM910006", "GSM910007", "GSM910008", "GSM910009", "GSM910010", "GSM910011", "GSM910012", "GSM910013", "GSM910014", "GSM910015", "GSM910016", "GSM910017", "GSM910018", "GSM910019", "GSM910020", "GSM910021", "GSM910022", "GSM910023", "GSM910024", "GSM910025", "GSM910026", "GSM910027", "GSM910028", "GSM910029", "GSM910030", "GSM910031", "GSM910032", "GSM910033", "GSM910034", "GSM910035", "GSM910036", "GSM910037", "GSM910038", "GSM910039", "GSM910040", "GSM910041", "GSM910042", "GSM910043", "GSM910044", "GSM910045", "GSM910046", "GSM910047", "GSM910048", "GSM910049", "GSM910050", "GSM910051", "GSM910052", "GSM910053", "GSM910054", "GSM910055", "GSM910056", "GSM910057", "GSM910058", "GSM910059", "GSM910060", "GSM910061", "GSM910062", "GSM910063", "GSM910064", "GSM910065", "GSM910066", "GSM910067", "GSM910068", "GSM910069", "GSM910070", "GSM910071", "GSM910072", "GSM910073", "GSM910074", "GSM910075", "GSM910076", "GSM910077", "GSM910078", "GSM910079", "GSM910080", "GSM910081", "GSM910082", "GSM910083", "GSM910084", "GSM910085", "GSM910086", "GSM910087", "GSM910088", "GSM910089", "GSM910090", "GSM910091", "GSM910092", "GSM910093", "GSM910094", "GSM910095", "GSM910096", "GSM910097", "GSM910098", "GSM910099", "GSM910100", "GSM910101", "GSM910102", "GSM910103", "GSM910104", "GSM910105", "GSM910106", "GSM910107", "GSM910108", "GSM910109", "GSM910110", "GSM910111", "GSM910112", "GSM910113", "GSM910114", "GSM910115", "GSM910116", "GSM910117", "GSM910118", "GSM910119", "GSM910120", "GSM910121", "GSM910122", "GSM910123", "GSM910124", "GSM910125", "GSM910126", "GSM910127", "GSM910128", "GSM910129", "GSM910130", "GSM910131", "GSM910132", "GSM910133", "GSM910134", "GSM910135", "GSM910136", "GSM910137", "GSM910138", "GSM910139", "GSM910140", "GSM910141", "GSM910142", "GSM910143", "GSM910144", "GSM910145", "GSM910146", "GSM910147", "GSM910148", "GSM910149", "GSM910150", "GSM910151", "GSM910152", "GSM910153", "GSM910154", "GSM910155", "GSM910156", "GSM910157", "GSM910158", "GSM910159", "GSM910160", "GSM910161", "GSM910162", "GSM910163", "GSM910164", "GSM910165", "GSM910166", "GSM910167", "GSM910168", "GSM910169", "GSM910170", "GSM910171", "GSM910172", "GSM910173", "GSM910174", "GSM910175", "GSM910176", "GSM910177", "GSM910178", "GSM910179", "GSM910180", "GSM910181", "GSM910182", "GSM910183", "GSM910184", "GSM910185", "GSM910186", "GSM910187", "GSM910188", "GSM910189", "GSM910190", "GSM910191", "GSM910192", "GSM910193", "GSM910194", "GSM910195", "GSM910196", "GSM910197", "GSM910198", "GSM910199", "GSM910200", "GSM910201", "GSM910202", "GSM910203", "GSM910204", "GSM910205", "GSM910206", "GSM910207", "GSM910208", "GSM910209", "GSM910210", "GSM910211", "GSM910212", "GSM910213", "GSM910214", "GSM910215", "GSM910216", "GSM910217", "GSM910218", "GSM910219", "GSM910220", "GSM910221", "GSM910222", "GSM910223", "GSM910224", "GSM910225", "GSM910226", "GSM910227", "GSM910228", "GSM910229", "GSM910230", "GSM910231", "GSM910232", "GSM910233"], "sample_count": 590, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene response to major burn injuries", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE8056", "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=GSE8056", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE8056", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM198866", "GSM198867", "GSM198868", "GSM198869", "GSM198870", "GSM198871", "GSM198872", "GSM198873", "GSM198874", "GSM198875", "GSM198876", "GSM198877"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Profiles in Thermally Injured Human Skin: A Temporal Microarray Analysis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE123568 not downloaded", "asset:data:geo:GSE123568 licence not read", "asset:data:geo:GSE13902 not downloaded", "asset:data:geo:GSE13902 licence not read", "asset:data:geo:GSE139028 not downloaded", "asset:data:geo:GSE139028 licence not read", "asset:data:geo:GSE19743 not downloaded", "asset:data:geo:GSE19743 licence not read", "asset:data:geo:GSE37069 not downloaded", "asset:data:geo:GSE37069 licence not read", "asset:data:geo:GSE8056 not downloaded", "asset:data:geo:GSE8056 licence not read"]}, "analysis": {"state": "partial", "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": "pathway enrichment"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC Analysis"}}, {"id": "method-4", "family": null, "specific": null, "label": "Weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Weighted gene co-expression network analysis (WGCNA) (Langfelder and Horvath, 2008), a novel systems biology method, assists in the construction of free-scale gene co-expression networks and the detection of gene modules and hub genes."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE8056", "GSE19743", "GSE37069", "GSE139028", "GSE13902", "GSE123568"], "resolved_accessions": ["GSE8056", "GSE19743", "GSE37069", "GSE139028", "GSE13902", "GSE123568"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE8056, GSE19743, GSE37069, GSE139028, GSE13902, GSE123568 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:35047008", "data:geo:GSE123568"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE123568"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:16:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11131, "completion_tokens": 2361, "cached_tokens": 0}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35047008", "type": "paper", "label": "pmid:35047008"}, {"id": "source:pmid:35047008", "type": "manuscript", "label": "PMID 35047008 full text"}, {"id": "data:geo:GSE123568", "type": "dataset", "label": "GEO GSE123568"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35047008", "type": "paper", "label": "pmid:35047008"}, {"id": "source:pmid:35047008", "type": "manuscript", "label": "PMID 35047008 full text"}, {"id": "data:geo:GSE123568", "type": "dataset", "label": "GEO GSE123568"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35047008", "type": "extraction", "used": ["source:pmid:35047008"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE123568", "type": "accession_resolution", "used": ["data:geo:GSE123568"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35047008", "parent_hash": "sha256:4195b9ac7f2a191ace4475771eaae4f4dc804081a80331065ab8aee3c4a671fe", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE123568 licence not read", "asset:data:geo:GSE123568 not downloaded", "asset:data:geo:GSE13902 licence not read", "asset:data:geo:GSE13902 not downloaded", "asset:data:geo:GSE139028 licence not read", "asset:data:geo:GSE139028 not downloaded", "asset:data:geo:GSE19743 licence not read", "asset:data:geo:GSE19743 not downloaded", "asset:data:geo:GSE37069 licence not read", "asset:data:geo:GSE37069 not downloaded", "asset:data:geo:GSE8056 licence not read", "asset:data:geo:GSE8056 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lidated in two other GEO datasets, tested by immunohistochemistry for hub gene expression in burn patients, an", "902 datasets. Furthermore, we verified using immunohistochemistry that these five novel hub genes were also si", "e Collection of Patient Tissue Specimens and IHC Staining We collected 13 burn patient skin s", "dded skin tissues were sectioned at 4 μm for IHC. Antigen retrieval was performed by incubati"], "order_basis": "paper_text_order:1105", "id": "assay:1"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["y five potential novel diagnostic markers in blood samples from burn patients, which are important for burn"], "order_basis": "paper_text_order:2479", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}