Identification of Common Differentially Expressed Genes and Potential Therapeutic Targets in Ulcerative Colitis and Rheumatoid Arthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33262784", "kind": "science-record", "revision": 7, "content_hash": "sha256:6975fb487aafbcbf89ac266a7c93ce352290a43b7c43117b48050ba39e188ea9", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T22:02:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Common Differentially Expressed Genes and Potential Therapeutic Targets in Ulcerative Colitis and Rheumatoid Arthritis.", "doi": "10.3389/fgene.2020.572194", "pmid": "33262784", "authors": ["Yueying Chen", "Hanyang Li", "Lijie Lai", "Qi Feng", "Jun Shen"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "Ulcerative colitis (UC) and rheumatoid arthritis (RA) are immune-mediated inflammatory diseases (IMIDs) with similar symptoms and common genomics. However, the relationship between UC and RA has not been investigated thoroughly. Therefore, this study aimed to establish the differentially expressed genes (DEGs) and potential therapeutic targets in UC and RA. Three microarray datasets (GSE38713, GSE1919, and GSE12251) were selected from the Gene Expression Omnibus (GEO) database for analysis. We used R software to identify the DEGs and performed enrichment analyses. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape software were used to construct the protein-protein interaction (PPI) network and identify the hub genes. A regulatory network based on the constructed PPI was generated using StarBase and PROMO databases. We identified a total of 1542 and 261 DEGs in UC and RA. There were 169 common DEGs identified in both UC and RA, including 63 upregulated genes (DEGs1) and nine downregulated genes (DEGs2). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs1 and DEGs2 in the PPI network revealed that the genes enriched were involved in immunity. A total of 45 hub genes were selected based on high scores of correlation; three hub genes (SRGN, PLEK, and FCGR3B) were found to be upregulated in UC and RA, and downregulated in UC patients with response to infliximab treatment. The identification of novel DEGs and hub genes in the current study contributes to a novel perception for latent functional mechanisms and presents potential prognostic indicators and therapeutic targets in UC and RA.", "claims": [{"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33262784", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33262784"], "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:GSE12251"], "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:GSE12251"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33262784", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.572194", "sha256": "sha256:05c5d7885158065d06a4776f634fb1e5e88342cc9ead9ffca01f21cff6214abe", "bytes": 39572, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2020.572194", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7686785", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12251", "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=GSE12251", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12251", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM307886", "GSM307887", "GSM307888", "GSM307889", "GSM307890", "GSM307891", "GSM307892", "GSM307893", "GSM307894", "GSM307895", "GSM307896", "GSM307897", "GSM307898", "GSM307899", "GSM307900", "GSM307901", "GSM307902", "GSM307903", "GSM307904", "GSM307905", "GSM307906", "GSM307907", "GSM307908"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A Predictive Response Signature to Infliximab Treatment in Ulcerative Colitis", "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:GSE1919", "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=GSE1919", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1919", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM34379", "GSM34383", "GSM34385", "GSM34388", "GSM34391", "GSM34393", "GSM34394", "GSM34395", "GSM34396", "GSM34397", "GSM34398", "GSM34399", "GSM34400", "GSM34401", "GSM34402"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "91", "taxon": "Homo sapiens", "title": "Rheumatoid arthritis", "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:GSE38713", "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=GSE38713", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38713", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM948550", "GSM948551", "GSM948552", "GSM948553", "GSM948554", "GSM948555", "GSM948556", "GSM948557", "GSM948558", "GSM948559", "GSM948560", "GSM948561", "GSM948562", "GSM948563", "GSM948564", "GSM948565", "GSM948566", "GSM948567", "GSM948568", "GSM948569", "GSM948570", "GSM948571", "GSM948572", "GSM948573", "GSM948574", "GSM948575", "GSM948576", "GSM948577", "GSM948578", "GSM948579", "GSM948580", "GSM948581", "GSM948582", "GSM948583", "GSM948584", "GSM948585", "GSM948586", "GSM948587", "GSM948588", "GSM948589", "GSM948590", "GSM948591", "GSM948592"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from intestinal mucosa of patients with UC", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33262784:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:239037b91e64b5a4109346b26be08c6504dd9c14f2886837f35c2afbb4fc65a8", "bytes": 1536, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T1", "version": null, "note": "The GO enrichment analysis of DEGs3 and DEGs4 (top 3 terms according to p.adjust).", "structure": {"pmcid": "PMC7686785", "section_index": 11, "section_title": "GO Enrichment Analyses of Independent DEGs in UC and RA", "row_count": 19, "column_count": 6}, "table": {"label": "TABLE 1", "caption": "The GO enrichment analysis of DEGs3 and DEGs4 (top 3 terms according to p.adjust).", "rows": [["DEGs", "Ontology", "ID", "Description", "Count", "p.adjust"], ["DEGs3", "BP", "GO:0050900", "Leukocyte migration", "138", "3.44E-41"], ["", "", "GO:0006959", "Humoral immune response", "110", "2.09E-37"], ["", "", "GO:0050727", "Regulation of inflammatory response", "120", "1.06E-30"], ["", "CC", "GO:0062023", "Collagen-containing extracellular matrix", "109", "2.07E-32"], ["", "", "GO:0009897", "External side of plasma membrane", "98", "1.92E-26"], ["", "", "GO:0019814", "Immunoglobulin complex", "53", "3.78E-20"], ["", "MF", "GO:0003823", "Antigen binding", "57", "1.83E-21"], ["", "", "GO:0005201", "Extracellular matrix structural constituent", "47", "1.61E-13"], ["", "", "GO:0034987", "Immunoglobulin receptor binding", "31", "2.48E-13"], ["DEGs4", "BP", "GO:0046677", "Response to antibiotic", "14", "0.000109"], ["", "", "GO:0051384", "Response to glucocorticoid", "10", "0.000109"], ["", "", "GO:0031960", "Response to corticosteroid", "10", "0.000193"], ["", "CC", "GO:0009897", "External side of plasma membrane", "16", "1.88E-06"], ["", "", "GO:0044449", "Contractile fiber part", "8", "0.008248"], ["", "", "GO:0030665", "Clathrin-coated vesicle membrane", "6", "0.008248"], ["", "MF", "GO:0001227", "DNA-binding transcription repressor activity", "8", "0.000361"], ["", "", "GO:0015026", "Coreceptor activity", "5", "0.005158"], ["", "", "GO:0001618", "Virus receptor activity", "5", "0.020157"]], "row_count": 19, "column_count": 6, "numeric_cells": 54, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE12251 not downloaded", "asset:data:geo:GSE12251 licence not read", "asset:data:geo:GSE1919 not downloaded", "asset:data:geo:GSE1919 licence not read", "asset:data:geo:GSE38713 not downloaded", "asset:data:geo:GSE38713 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE38713", "GSE1919", "GSE12251"], "resolved_accessions": ["GSE38713", "GSE1919", "GSE12251"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE38713, GSE1919, GSE12251 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": ["pearson_r"], "assets": ["source:pmid:33262784", "data:geo:GSE12251", "asset:table:pmid:33262784:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12251"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:17:26Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34196, "completion_tokens": 1620, "cached_tokens": 784}}, "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:33262784", "type": "paper", "label": "pmid:33262784"}, {"id": "source:pmid:33262784", "type": "manuscript", "label": "PMID 33262784 full text"}, {"id": "data:geo:GSE12251", "type": "dataset", "label": "GEO GSE12251"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33262784", "type": "paper", "label": "pmid:33262784"}, {"id": "source:pmid:33262784", "type": "manuscript", "label": "PMID 33262784 full text"}, {"id": "data:geo:GSE12251", "type": "dataset", "label": "GEO GSE12251"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33262784", "type": "extraction", "used": ["source:pmid:33262784"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12251", "type": "accession_resolution", "used": ["data:geo:GSE12251"], "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:33262784", "parent_hash": "sha256:5f0436701f914441bedb9b98d0727e6f61c0d31b2938b3de8528478e11fd15e7", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE12251 licence not read", "asset:data:geo:GSE12251 not downloaded", "asset:data:geo:GSE1919 licence not read", "asset:data:geo:GSE1919 not downloaded", "asset:data:geo:GSE38713 licence not read", "asset:data:geo:GSE38713 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": ["tial therapeutic targets in UC and RA. Three microarray datasets (GSE38713, GSE1919, and GSE12251) w"], "order_basis": "paper_text_order:459", "id": "assay:1"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Pearson correlation"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}