Identification of Significant Genes and Pathways for the Chronic and Subacute Cutaneous Lupus Erythematosus via Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36212172", "kind": "science-record", "revision": 4, "content_hash": "sha256:74d2bc9a7575b88cdc03db3da8e46a19513c9c679174fef79cf84423e7379a58", "created_at": "2026-11-01T18:15:33Z", "updated_at": "2026-11-01T22:07:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Significant Genes and Pathways for the Chronic and Subacute Cutaneous Lupus Erythematosus via Bioinformatics Analysis.", "doi": "10.1155/2022/9891299", "pmid": "36212172", "authors": ["Yan Teng", "Sujing Li", "Yang Ding", "Yibin Fan", "Miao He", "Hengzhen Li", "Xiaohua Tao", "Youming Huang"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Chronic cutaneous lupus erythematosus (CCLE) and subacute cutaneous lupus erythematosus (SCLE) are both common variants of cutaneous lupus erythematosus (CLE) that mainly involve the skin and mucous membrane. Oral mucosal involvement is frequently observed in patients of CLE. Despite that they have different clinicopathological features, whether there is a significant difference in pathogenesis between them remains unclear. Herein, we investigated specific genes and pathways of SCLE and CCLE via bioinformatics analysis.\nMethods: Microarray expression datasets of GSE109248 and GSE112943 were both retrieved from the GEO database. Differentially expressed genes (DEGs) between CCLE or SCLE skin tissues and health controls were selected by GEO2R. Common DEGs were picked out via the Venn diagram software. Then, functional enrichment and PPI network analysis were conducted, and the top 10 key genes were identified via Cytohubba.\nResults: Totally, 176 DEGs of SCLE and 287 DEGs of CCLE were identified. The GO enrichment and KEGG analysis of DEGs of SCLE is significantly enriched in the response to virus, defense response to virus, response to IFN-gamma, cellular response to IFN-γ, type I IFN signaling pathway, chemokine activity, chemokine receptor binding, NOD-like receptor signaling pathway, etc. The GO enrichment and KEGG analysis of DEGs of CCLE is significantly enriched in the response to virus, regulation of multiorganism process, negative regulation of viral process, regulation of lymphocyte activation, chemokine receptor binding, CCR chemokine receptor binding, NOD-like receptor signaling pathway, etc. The top 10 hub genes of SCLE and CCLE, respectively, include STAT1, CXCL10, IRF7, ISG15, and RSAD2 and CXCL10, IRF7, IFIT3, CTLA4, and ISG15.\nConclusion: Our finding suggests that SCLE and CCLE have the similar potential key genes and pathways and majority of them belong to IFN signatures and IFN signaling pathway. Besides, the NOD-like receptor signaling pathway might also have an essential role in the pathogenesis of SCLE and CCLE. Together, the identified genes and signaling pathways have enhanced our understanding of the mechanism underlying the occurrence and development of both SCLE and CCLE.", "claims": [{"id": "claim-method", "statement": "The DEGs between CCLE and SCLE skin samples and skin control samples were identified via GEO2R online tool via the standard |LogFC| > 2 and adjusted P value < 0.05 [11].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36212172", "locator": "sections[4] \"2.2. Data Processing of DEGs\" paragraph 2", "quote": "The DEGs between CCLE and SCLE skin samples and skin control samples were identified via GEO2R online tool via the standard |LogFC| > 2 and adjusted P value < 0.05 [11]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GSE109248 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109248) and in the GSE112943 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112943).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36212172", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GSE109248 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109248) and in the GSE112943 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112943)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our finding suggests that SCLE and CCLE have the similar potential key genes and pathways and majority of them belong to IFN signatures and IFN signaling pathway.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36212172", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our finding suggests that SCLE and CCLE have the similar potential key genes and pathways and majority of them belong to IFN signatures and IFN signaling pathway."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our finding suggests that SCLE and CCLE have the similar potential key genes and pathways and majority of them belong to IFN signatures and IFN signaling pathway.", "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:36212172"], "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:GSE109248"], "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:GSE109248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36212172", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/9891299", "sha256": 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(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109248) and in the GSE112943 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112943).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GSE109248 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109248) and in the GSE112943 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112943).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2935828", "GSM2935829", "GSM2935830", "GSM2935831", "GSM2935832", "GSM2935833", "GSM2935834", "GSM2935835", "GSM2935836", "GSM2935837", "GSM2935838", "GSM2935839", "GSM2935840", "GSM2935841", "GSM2935842", "GSM2935843", "GSM2935844", "GSM2935845", "GSM2935846", "GSM2935847", "GSM2935848", "GSM2935849", "GSM2935850", "GSM2935851", "GSM2935852", "GSM2935853", "GSM2935854", "GSM2935855", 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null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE112943", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GSE109248 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109248) and in the GSE112943 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112943).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GSE109248 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109248) and in the GSE112943 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112943).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3091745", "GSM3091746", "GSM3091747", "GSM3091748", "GSM3091749", "GSM3091750", "GSM3091751", "GSM3091752", "GSM3091753", 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:36212172", "data:geo:GSE109248"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE109248"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:09:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9003, "completion_tokens": 2192, "cached_tokens": 264}}, "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:36212172", "type": "paper", "label": "pmid:36212172"}, {"id": "source:pmid:36212172", "type": "manuscript", "label": "PMID 36212172 full text"}, {"id": "data:geo:GSE109248", "type": "dataset", "label": "GEO GSE109248"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36212172", "type": "paper", "label": "pmid:36212172"}, {"id": "source:pmid:36212172", "type": "manuscript", "label": "PMID 36212172 full text"}, {"id": "data:geo:GSE109248", "type": "dataset", "label": "GEO GSE109248"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36212172", "type": "extraction", "used": ["source:pmid:36212172"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE109248", "type": "accession_resolution", "used": ["data:geo:GSE109248"], "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:36212172", "parent_hash": "sha256:d94727e15681dae90c9b7d99244d5a700b6513eb6caa717baf977bf00f5774f7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE109248 licence not read", "asset:data:geo:GSE109248 not downloaded", "asset:data:geo:GSE112943 licence not read", "asset:data:geo:GSE112943 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["d CCLE via bioinformatics analysis. 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