← All .science files
pmid:37935955
Exploring the molecular mechanism underlying the psoriasis and T2D by using microarray data analysis.
Li Yang · Lei Zhang · Qingfang Du · Xiaoyu Gong · Jun Tian
Scientific reports · 2023 doi:10.1038/s41598-023-46795-5
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 5 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
[2] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 13 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 170 items
gaps array · 4 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37935955", "kind": "science-record", "revision": 4, "content_hash": "sha256:4e35e1fb1881f960c5d98c6ad0d3f5de8b7dbc623aa6d2265eb8fae065ebcb59", "created_at": "2026-11-01T19:02:49Z", "updated_at": "2026-11-01T22:53:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the molecular mechanism underlying the psoriasis and T2D by using microarray data analysis.", "doi": "10.1038/s41598-023-46795-5", "pmid": "37935955", "authors": ["Li Yang", "Lei Zhang", "Qingfang Du", "Xiaoyu Gong", "Jun Tian"], "journal": "Scientific reports", "year": 2023, "abstract": "Although a large number of evidence has identified that psoriasis is significantly correlated with type 2 diabetes (T2D), the common molecular mechanism of its occurrence remains unclear. Our study aims to further elucidate the mechanism of the occurrence of this complication. We obtained the gene expression data of psoriasis (GSE30999) and T2D (GSE28829) from the Gene Expression Omnibus (GEO) dataset. Then the common differentially expressed genes (DEGs) of T2D and psoriasis were identified. After that, we performed three types of analyses about these DEGs, including functional enrichment analysis, protein-protein interaction (PPI) network and module manufacture, hub genes identification and co-expression analysis. 132 common DEGs (14 upregulated genes and 118 downregulated genes) were identified for subsequent a series of analyses. Function enrichment analysis demonstrated that Rap1 signaling pathway, PI3K-Akt signaling pathway, and cGMP-PKG signaling pathway may play a significant role in pathogenesis of psoriasis and T2D. Finally, 3 important hub genes were selected by utilizing cytoHubba, including SNRPN, GNAS, IGF2. Our work reveals the potential common signaling pathways of psoriasis and T2D. These Hub genes and common signaling pathways provide insights for further investigation of molecular mechanism about psoriasis and T2D.", "claims": [{"id": "claim-method", "statement": "GEO2R is a powerful online tool designed for gene expression analysis. This tool utilizes GEOquery and Limma R packages12.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37935955", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "GEO2R is a powerful online tool designed for gene expression analysis. This tool utilizes GEOquery and Limma R packages12."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37935955", "locator": "sections[22] \"Data availability\" paragraph 2", "quote": "The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 132 common differentially expressed genes between psoriasis and type 2 diabetes datasets, comprising 14 upregulated and 118 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37935955", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "132 common DEGs (14 upregulated genes and 118 downregulated genes) were identified for subsequent a series of analyses."}, {"asset": "source:pmid:37935955", "locator": "sections[12] \"Identification of DEGs\" paragraph 2", "quote": "Subsequently, 132 DEGs were obtained after excluding genes which had adverse expression trends in GSE25724 and GSE30999, containing 14 upregulated genes and 118 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 132 common differentially expressed genes between psoriasis and type 2 diabetes datasets, comprising 14 upregulated and 118 downregulated genes.", "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:37935955"], "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:GSE25724"], "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:GSE25724"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37935955", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-46795-5", "sha256": "sha256:71977ded809ffef1006235f63ebfbccd23e76d0fcaee61ee264954e90873bf75", "bytes": 46250, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-46795-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10630520", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25724", "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=GSE25724", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25724", "version": null, "note": "The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM631755", "GSM631756", "GSM631757", "GSM631758", "GSM631759", "GSM631760", "GSM631761", "GSM631762", "GSM631763", "GSM631764", "GSM631765", "GSM631766", "GSM631767"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from type 2 diabetic and non-diabetic isolated human islets", "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:GSE30999", "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=GSE30999", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30999", "version": null, "note": "The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM767976", "GSM767977", "GSM767978", "GSM767979", "GSM767980", "GSM767981", "GSM767982", "GSM767983", "GSM767984", "GSM767985", "GSM767986", "GSM767987", "GSM767988", "GSM767989", "GSM767990", "GSM767991", "GSM767992", "GSM767993", "GSM767994", "GSM767995", "GSM767996", "GSM767997", "GSM767998", "GSM767999", "GSM768000", "GSM768001", "GSM768002", "GSM768003", "GSM768004", "GSM768005", "GSM768006", "GSM768007", "GSM768008", "GSM768009", "GSM768010", "GSM768011", "GSM768012", "GSM768013", "GSM768014", "GSM768015", "GSM768016", "GSM768017", "GSM768018", "GSM768019", "GSM768020", "GSM768021", "GSM768022", "GSM768023", "GSM768024", "GSM768025", "GSM768026", "GSM768027", "GSM768028", "GSM768029", "GSM768030", "GSM768031", "GSM768032", "GSM768033", "GSM768034", "GSM768035", "GSM768036", "GSM768037", "GSM768038", "GSM768039", "GSM768040", "GSM768041", "GSM768042", "GSM768043", "GSM768044", "GSM768045", "GSM768046", "GSM768047", "GSM768048", "GSM768049", "GSM768050", "GSM768051", "GSM768052", "GSM768053", "GSM768054", "GSM768055", "GSM768056", "GSM768057", "GSM768058", "GSM768059", "GSM768060", "GSM768061", "GSM768062", "GSM768063", "GSM768064", "GSM768065", "GSM768066", "GSM768067", "GSM768068", "GSM768069", "GSM768070", "GSM768071", "GSM768072", "GSM768073", "GSM768074", "GSM768075", "GSM768076", "GSM768077", "GSM768078", "GSM768079", "GSM768080", "GSM768081", "GSM768082", "GSM768083", "GSM768084", "GSM768085", "GSM768086", "GSM768087", "GSM768088", "GSM768089", "GSM768090", "GSM768091", "GSM768092", "GSM768093", "GSM768094", "GSM768095", "GSM768096", "GSM768097", "GSM768098", "GSM768099", "GSM768100", "GSM768101", "GSM768102", "GSM768103", "GSM768104", "GSM768105", "GSM768106", "GSM768107", "GSM768108", "GSM768109", "GSM768110", "GSM768111", "GSM768112", "GSM768113", "GSM768114", "GSM768115", "GSM768116", "GSM768117", "GSM768118", "GSM768119", "GSM768120", "GSM768121", "GSM768122", "GSM768123", "GSM768124", "GSM768125", "GSM768126", "GSM768127", "GSM768128", "GSM768129", "GSM768130", "GSM768131", "GSM768132", "GSM768133", "GSM768134", "GSM768135", "GSM768136", "GSM768137", "GSM768138", "GSM768139", "GSM768140", "GSM768141", "GSM768142", "GSM768143", "GSM768144", "GSM768145"], "sample_count": 170, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from skin biopsy samples from patients with moderate-to-severe psoriasis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE30999 not downloaded", "asset:data:geo:GSE30999 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 is a powerful online tool designed for gene expression analysis. This tool utilizes GEOquery and Limma R packages12."}}, {"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": ["GSE30999", "GSE25724"], "resolved_accessions": ["GSE30999", "GSE25724"], "statements": ["The data which support the findings of our work are openly accessible from the GEO, STRING, GeneMANIA, and Cytoscape database."], "basis": "The paper names GSE30999, GSE25724 in Gene Expression Omnibus (GEO) 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:37935955", "data:geo:GSE25724"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE25724"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:58:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13433, "completion_tokens": 1596, "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:37935955", "type": "paper", "label": "pmid:37935955"}, {"id": "source:pmid:37935955", "type": "manuscript", "label": "PMID 37935955 full text"}, {"id": "data:geo:GSE25724", "type": "dataset", "label": "GEO GSE25724"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37935955", "type": "paper", "label": "pmid:37935955"}, {"id": "source:pmid:37935955", "type": "manuscript", "label": "PMID 37935955 full text"}, {"id": "data:geo:GSE25724", "type": "dataset", "label": "GEO GSE25724"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37935955", "type": "extraction", "used": ["source:pmid:37935955"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE25724", "type": "accession_resolution", "used": ["data:geo:GSE25724"], "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:37935955", "parent_hash": "sha256:34a07ae2915e4f65485260fec2df0e08e2cf0884c9daac57bd90b84342011d21", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE30999 licence not read", "asset:data:geo:GSE30999 not downloaded", "execution.not_run", "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": ["sm underlying the psoriasis and T2D by using microarray data analysis."], "order_basis": "paper_text_order:31", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["olutions. Reverse transcription kit and SYBR qPCR Master Mix (Shandong Sparkjade Biotechnology"], "order_basis": "paper_text_order:2716", "id": "assay:2"}, {"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 is a powerful online tool designed for gene expression analysis. This tool utilizes GEOquery and Limma R packages12."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}