Screening of key genes related to autophagy in psoriasis based on gene expression profiling.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39877103", "kind": "science-record", "revision": 3, "content_hash": "sha256:f07bab9727e5215954c53cf36626d3f775314524e400f5c288a9306d3c344ba2", "created_at": "2026-11-01T20:30:10Z", "updated_at": "2026-11-01T22:13:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of key genes related to autophagy in psoriasis based on gene expression profiling.", "doi": "10.5114/ada.2024.145618", "pmid": "39877103", "authors": ["Suo Mo", "Chunyan Cao", "Xiaoyue Dai", "Zhiwen Ding", "Yajuan Zuo", "Chuchu Song", "Xianfeng Cheng"], "journal": "Postepy dermatologii i alergologii", "year": 2024, "abstract": "Introduction: Autophagy is necessary for the progression of psoriasis.\nAim: This study aimed to recognize possible autophagy-related genes in psoriasis via bioinformatics study to present a better standard for the clinical treatment and management of psoriasis.\nMaterial and methods: The GEO dataset was utilized to derive the mRNA expression profile of the database GSE78097. R software was utilized to find autophagy-associated genes that may be expressed in psoriasis. Then, a protein-protein interaction (PPI) correlation study of the differentially expressed autophagy-associated genes was carried out, and GO and KEGG enrichment analysis was used to investigate any potential signalling pathways linked.\nResults: We identified a total of 156 autophagy-related genes in 27 psoriasis and 6 healthy skin tissue samples. The PPI network diagram findings demonstrate interactions among these autophagy-associated genes. Autophagy, protein processing, apoptosis, and mitochondria processes may be crucial in the development and occurrence of psoriasis suggested by KEGG and GO enrichment analysis.\nConclusions: Utilizing bioinformatics methods to recognize differentially expressed autophagy-related genes has further enhanced our understanding of psoriasis and provided new thinking for the study of the pathogenesis and therapeutic targets of psoriasis.", "claims": [{"id": "claim-method", "statement": "The R software tool was utilized to recognize differentially expressed autophagy-related genes. Absolute fold-change value > 1.5 and p-value < 0.05 were used to determine which genes were differentially expressed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39877103", "locator": "sections[4] \"Differential expression analysis of autophagy-associated genes\" paragraph 2", "quote": "The R software tool was utilized to recognize differentially expressed autophagy-related genes. Absolute fold-change value > 1.5 and p-value < 0.05 were used to determine which genes were differentially expressed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression profile of the GSE78097 dataset was downloaded from this database through the GEOquery package. GSE78097 is located in GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, which comprises 27 psoriasis and 6 normal skin tissue samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39877103", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "The expression profile of the GSE78097 dataset was downloaded from this database through the GEOquery package. GSE78097 is located in GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, which comprises 27 psoriasis and 6 normal skin tissue samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified a total of 156 autophagy-related genes in 27 psoriasis and 6 healthy skin tissue samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39877103", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We identified a total of 156 autophagy-related genes in 27 psoriasis and 6 healthy skin tissue samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified a total of 156 autophagy-related genes in 27 psoriasis and 6 healthy skin tissue samples.", "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:39877103"], "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:GSE78097"], "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:GSE78097"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39877103", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5114/ada.2024.145618", "sha256": "sha256:9d16b75e3eb273bef940934338c228fbdd4eddf0a1b10647031394025864a0e0", "bytes": 19359, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.5114/ada.2024.145618", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11770576", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE78097", "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=GSE78097", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE78097", "version": null, "note": "The expression profile of the GSE78097 dataset was downloaded from this database through the GEOquery package. 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GSE78097 is located in GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, which comprises 27 psoriasis and 6 normal skin tissue samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2066635", "GSM2066636", "GSM2066637", "GSM2066638", "GSM2066639", "GSM2066640", "GSM2066641", "GSM2066642", "GSM2066643", "GSM2066644", "GSM2066645", "GSM2066646", "GSM2066647", "GSM2066648", "GSM2066649", "GSM2066650", "GSM2066651", "GSM2066652", "GSM2066653", "GSM2066654", "GSM2066655", "GSM2066656", "GSM2066657", "GSM2066658", "GSM2066659", "GSM2066660", "GSM2066661", "GSM2066662", "GSM2066663", "GSM2066664", "GSM2066665", "GSM2066666", "GSM2066667"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "The spectrum of mild-to-severe psoriasis vulgaris is defined by a common activation of IL-17 pathway genes, but with key differences in immune regulatory genes", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE78097 not downloaded", "asset:data:geo:GSE78097 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The R software tool was utilized to recognize differentially expressed autophagy-related genes. 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