Transcriptome Analysis Identifies Biomarkers for the Diagnosis and Management of Psoriasis Complicated with Depression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37223217", "kind": "science-record", "revision": 4, "content_hash": "sha256:1b8eec4f12c42e0b84fa46338b52c75b5053835621afd12514aa4531a5eb4b28", "created_at": "2026-11-01T19:01:55Z", "updated_at": "2026-11-01T22:51:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome Analysis Identifies Biomarkers for the Diagnosis and Management of Psoriasis Complicated with Depression.", "doi": "10.2147/CCID.S413887", "pmid": "37223217", "authors": ["Xichun Xia", "Hai Yu", "Yanxiang Li", "Yunting Liang", "Guangqiang Li", "Fang Huang"], "journal": "Clinical, cosmetic and investigational dermatology", "year": 2023, "abstract": "Purpose: Psoriasis is a systemic inflammatory disease, and the mechanism that links psoriasis to depression is still elusive. Hence, this study aimed to elucidate the potential pathogenesis of psoriasis and depression comorbidity.\nMethods: The gene expression profiles of psoriasis (GSE34248, GSE78097 and GSE161683) and depression (GSE39653) were downloaded from the Gene Expression Omnibus (GEO) DataSets. Functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis were performed, following identification of the common differentially expressed genes (DEGs) of psoriasis and depression.\nResults: A total of 115 common DEGs (55 up-regulated and 60 down-regulated) were identified between psoriasis and depression. Functional analysis indicated that T cell activation and differentiation were predominantly implicated in the potential pathogenesis of these two diseases. In addition, Th17 cell differentiation and cytokines is closely related to both. Finally, 17 hub genes were screened, including CTLA4, LCK, ITK, IL7R, CD3D, SOCS1, IL4R, PRKCQ, SOCS3, IL23A, PDGFB, PAG1, TGFA, FGFR1, RELN, ITGB5 and TNXB, which re-emphasized the importance of the immune system in psoriasis and depression.\nConclusion: Our study reveals the common pathogenesis of psoriasis and depression. These common pathways and hub genes may apply to a molecular screening tool for depression in psoriasis patients, which could help dermatologists optimize patient management in routine care.", "claims": [{"id": "claim-method", "statement": "GEO2R (www.ncbi.nlm.nih.gov/geo/ge2r) is an interactive web tool developed based on GEOquery and Limma package. DEGs of psoriasis and depression group were respectively identified using GEO2R with adjusted P-value < 0.05 and |logFC (fold change)| ≥ 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37223217", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "GEO2R (www.ncbi.nlm.nih.gov/geo/ge2r) is an interactive web tool developed based on GEOquery and Limma package. DEGs of psoriasis and depression group were respectively identified using GEO2R with adjusted P-value < 0.05 and |logFC (fold change)| ≥ 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37223217", "locator": "sections[3] \"Data Source\" paragraph 2", "quote": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 115 common differentially expressed genes between psoriasis and depression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37223217", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 115 common DEGs (55 up-regulated and 60 down-regulated) were identified between psoriasis and depression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 115 common differentially expressed genes between psoriasis and depression.", "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:37223217"], "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:GSE137218"], "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:GSE137218"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37223217", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CCID.S413887", "sha256": "sha256:50c793517143e925bd6ef60f3dad3a418873b6463d5467c55689c7ee987fca69", "bytes": 47640, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CCID.S413887", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10202145", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE137218", "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=GSE137218", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE137218", "version": null, "note": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4073326", "GSM4073327", "GSM4073328", "GSM4073329", "GSM4073330", "GSM4073331", "GSM4073332", "GSM4073333", "GSM4073334", "GSM4073335", "GSM4073336", "GSM4073337", "GSM4073338", "GSM4073339", "GSM4073340", "GSM4073341", "GSM4073342", "GSM4073343", "GSM4073344", "GSM4073345", "GSM4073346", "GSM4073347", "GSM4073348", "GSM4073349", "GSM4073350", "GSM4073351", "GSM4073352", "GSM4073353", "GSM4073354", "GSM4073355", "GSM4073356", "GSM4073357", "GSM4073358", "GSM4073359", "GSM4073360", "GSM4073361", "GSM4073362", "GSM4073363", "GSM4073364", "GSM4073365", "GSM4073366", "GSM4073367", "GSM4073368", "GSM4073369", "GSM4073370", "GSM4073371", "GSM4073372", "GSM4073373", "GSM4073374", "GSM4073375", "GSM4073376", "GSM4073377", "GSM4073378", "GSM4073379", "GSM4073380", "GSM4073381", "GSM4073382", "GSM4073383", "GSM4073384", "GSM4073385", "GSM4073386", "GSM4073387", "GSM4073388", "GSM4073389", "GSM4073390", "GSM4073391", "GSM4073392", "GSM4073393", "GSM4073394", "GSM4073395", "GSM4073396", "GSM4073397", "GSM4073398", "GSM4073399", "GSM4073400", "GSM4073401", "GSM4073402", "GSM4073403", "GSM4073404", "GSM4073405", "GSM4073406", "GSM4073407", "GSM4073408", "GSM4073409"], "sample_count": 84, "group_sizes": null, "group_sizes_basis": null, "platform": "23126", "taxon": "Homo sapiens", "title": "Skin expression data from psoriasis patients treated with secukinumab", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE161683", "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=GSE161683", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE161683", "version": null, "note": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4912653", "GSM4912654", "GSM4912655", "GSM4912656", "GSM4912657", "GSM4912658", "GSM4912659", "GSM4912660", "GSM4912661", "GSM4912662", "GSM4912663", "GSM4912664", "GSM4912665", "GSM4912666", "GSM4912667", "GSM4912668", "GSM4912669", "GSM4912670"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from lesional (LP) and non-lesional (NP) skin in patients with psoriasis.", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE34248", "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=GSE34248", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34248", "version": null, "note": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM845740", "GSM845741", "GSM845742", "GSM845743", "GSM845744", "GSM845745", "GSM845746", "GSM845747", "GSM845748", "GSM845749", "GSM845750", "GSM845751", "GSM845752", "GSM845753", "GSM845754", "GSM845755", "GSM845756", "GSM845757", "GSM845758", "GSM845759", "GSM845760", "GSM845761", "GSM845762", "GSM845763", "GSM845764", "GSM845765", "GSM845766", "GSM845767"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling in psoriatic lesional and non-lesional skin [Set 1]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39653", "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=GSE39653", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39653", "version": null, "note": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM973762", "GSM973763", "GSM973764", "GSM973765", "GSM973766", "GSM973767", "GSM973768", "GSM973769", "GSM973770", "GSM973771", "GSM973772", "GSM973773", "GSM973774", "GSM973775", "GSM973776", "GSM973777", "GSM973778", "GSM973779", "GSM973780", "GSM973781", "GSM973782", "GSM973783", "GSM973784", "GSM973785", "GSM973786", "GSM973787", "GSM973788", "GSM973789", "GSM973790", "GSM973791", "GSM973792", "GSM973793", "GSM973794", "GSM973795", "GSM973796", "GSM973797", "GSM973798", "GSM973799", "GSM973800", "GSM973801", "GSM973802", "GSM973803", "GSM973804", "GSM973805", "GSM973806", "GSM973807", "GSM973808", "GSM973809", "GSM973810", "GSM973811", "GSM973812", "GSM973813", "GSM973814"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Differential Gene Expression in Patients with Mood Disorders", "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: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": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "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}}, {"id": "data:geo:GSE98793", "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=GSE98793", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98793", "version": null, "note": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2612096", "GSM2612097", "GSM2612098", "GSM2612099", "GSM2612100", "GSM2612101", "GSM2612102", "GSM2612103", "GSM2612104", "GSM2612105", "GSM2612106", "GSM2612107", "GSM2612108", "GSM2612109", "GSM2612110", "GSM2612111", "GSM2612112", "GSM2612113", "GSM2612114", "GSM2612115", "GSM2612116", "GSM2612117", "GSM2612118", "GSM2612119", "GSM2612120", "GSM2612121", "GSM2612122", "GSM2612123", "GSM2612124", "GSM2612125", "GSM2612126", "GSM2612127", "GSM2612128", "GSM2612129", "GSM2612130", "GSM2612131", "GSM2612132", "GSM2612133", "GSM2612134", "GSM2612135", "GSM2612136", "GSM2612137", "GSM2612138", "GSM2612139", "GSM2612140", "GSM2612141", "GSM2612142", "GSM2612143", "GSM2612144", "GSM2612145", "GSM2612146", "GSM2612147", "GSM2612148", "GSM2612149", "GSM2612150", "GSM2612151", "GSM2612152", "GSM2612153", "GSM2612154", "GSM2612155", "GSM2612156", "GSM2612157", "GSM2612158", "GSM2612159", "GSM2612160", "GSM2612161", "GSM2612162", "GSM2612163", "GSM2612164", "GSM2612165", "GSM2612166", "GSM2612167", "GSM2612168", "GSM2612169", "GSM2612170", "GSM2612171", "GSM2612172", "GSM2612173", "GSM2612174", "GSM2612175", "GSM2612176", "GSM2612177", "GSM2612178", "GSM2612179", "GSM2612180", "GSM2612181", "GSM2612182", "GSM2612183", "GSM2612184", "GSM2612185", "GSM2612186", "GSM2612187", "GSM2612188", "GSM2612189", "GSM2612190", "GSM2612191", "GSM2612192", "GSM2612193", "GSM2612194", "GSM2612195", "GSM2612196", "GSM2612197", "GSM2612198", "GSM2612199", "GSM2612200", "GSM2612201", "GSM2612202", "GSM2612203", "GSM2612204", "GSM2612205", "GSM2612206", "GSM2612207", "GSM2612208", "GSM2612209", "GSM2612210", "GSM2612211", "GSM2612212", "GSM2612213", "GSM2612214", "GSM2612215", "GSM2612216", "GSM2612217", "GSM2612218", "GSM2612219", "GSM2612220", "GSM2612221", "GSM2612222", "GSM2612223", "GSM2612224", "GSM2612225", "GSM2612226", "GSM2612227", "GSM2612228", "GSM2612229", "GSM2612230", "GSM2612231", "GSM2612232", "GSM2612233", "GSM2612234", "GSM2612235", "GSM2612236", "GSM2612237", "GSM2612238", "GSM2612239", "GSM2612240", "GSM2612241", "GSM2612242", "GSM2612243", "GSM2612244", "GSM2612245", "GSM2612246", "GSM2612247", "GSM2612248", "GSM2612249", "GSM2612250", "GSM2612251", "GSM2612252", "GSM2612253", "GSM2612254", "GSM2612255", "GSM2612256", "GSM2612257", "GSM2612258", "GSM2612259", "GSM2612260", "GSM2612261", "GSM2612262", "GSM2612263", "GSM2612264", "GSM2612265", "GSM2612266", "GSM2612267", "GSM2612268", "GSM2612269", "GSM2612270", "GSM2612271", "GSM2612272", "GSM2612273", "GSM2612274", "GSM2612275", "GSM2612276", "GSM2612277", "GSM2612278", "GSM2612279", "GSM2612280", "GSM2612281", "GSM2612282", "GSM2612283", "GSM2612284", "GSM2612285", "GSM2612286", "GSM2612287"], "sample_count": 192, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis in whole blood samples obtained from donors diagnosed with MDD compared to healthy controls", "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:GSE137218 not downloaded", "asset:data:geo:GSE137218 licence not read", "asset:data:geo:GSE161683 not downloaded", "asset:data:geo:GSE161683 licence not read", "asset:data:geo:GSE34248 not downloaded", "asset:data:geo:GSE34248 licence not read", "asset:data:geo:GSE39653 not downloaded", "asset:data:geo:GSE39653 licence not read", "asset:data:geo:GSE78097 not downloaded", "asset:data:geo:GSE78097 licence not read", "asset:data:geo:GSE98793 not downloaded", "asset:data:geo:GSE98793 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "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": "GEO2R (www.ncbi.nlm.nih.gov/geo/ge2r) is an interactive web tool developed based on GEOquery and Limma package. DEGs of psoriasis and depression group were respectively identified using GEO2R with adjusted P-value < 0.05 and |logFC (fold change)| ≥ 1."}}, {"id": "method-2", "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-3", "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"}}], "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: limma_voom."}, "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": ["GSE34248", "GSE78097", "GSE161683", "GSE39653", "GSE137218", "GSE98793"], "resolved_accessions": ["GSE34248", "GSE78097", "GSE161683", "GSE39653", "GSE137218", "GSE98793"], "statements": ["GSE34248 (14 psoriasis patients and 14 controls), GSE78097 (13 psoriasis patients and 6 controls), GSE161683 (9 psoriasis patients and 9 controls) and GSE137218 (14 psoriasis patients and 14 controls) were screened as psoriasis datasets,28–30 in which the tissue type is skin lesion from psoriasis patients. Meanwhile, GSE39653 (24 depression patients and 21 controls) and GSE98793 (64 depression patients and 64 controls) were screened as depression datasets,31,32 in which the tissue type is peripheral blood mononuclear cells (PBMC) from patients with depression. GSE34248, GSE78097, GSE161683 and GSE39653 were used to screen DEGs, while GSE137218 and GSE98793 were used for hub gene expression validation."], "basis": "The paper names GSE34248, GSE78097, GSE161683, GSE39653, GSE137218, GSE98793 in Gene Expression Omnibus (GEO) DataSets and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37223217", "data:geo:GSE137218"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE137218"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:41:33Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 13732, "completion_tokens": 2625, "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:37223217", "type": "paper", "label": "pmid:37223217"}, {"id": "source:pmid:37223217", "type": "manuscript", "label": "PMID 37223217 full text"}, {"id": "data:geo:GSE137218", "type": "dataset", "label": "GEO GSE137218"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37223217", "type": "paper", "label": "pmid:37223217"}, {"id": "source:pmid:37223217", "type": "manuscript", "label": "PMID 37223217 full text"}, {"id": "data:geo:GSE137218", "type": "dataset", "label": "GEO GSE137218"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37223217", "type": "extraction", "used": ["source:pmid:37223217"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE137218", "type": "accession_resolution", "used": ["data:geo:GSE137218"], "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:37223217", "parent_hash": "sha256:274cc4f196bec8169eb1ee679694f343a649466997f74afdf48acdae122e0ec1", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE137218 licence not read", "asset:data:geo:GSE137218 not downloaded", "asset:data:geo:GSE161683 licence not read", "asset:data:geo:GSE161683 not downloaded", "asset:data:geo:GSE34248 licence not read", "asset:data:geo:GSE34248 not downloaded", "asset:data:geo:GSE39653 licence not read", "asset:data:geo:GSE39653 not downloaded", "asset:data:geo:GSE78097 licence not read", "asset:data:geo:GSE78097 not downloaded", "asset:data:geo:GSE98793 licence not read", "asset:data:geo:GSE98793 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["GEO2R (www.ncbi.nlm.nih.gov/geo/ge2r) is an interactive web tool developed based on GEOquery and Limma package. DEGs of psoriasis and depression group were respectively identified using GEO2R with adjusted P-value < 0.05 and |logFC (fold change)| ≥ 1."], "order_basis": "analysis_only", "id": "assay:1"}]}