Identification of Critical Modules and Biomarkers of Ulcerative Colitis by Using WGCNA.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37092131", "kind": "science-record", "revision": 3, "content_hash": "sha256:99651642a56ceffbf0d90bb0761d38a042b0d6d6c9e752933d036ed6022f69c1", "created_at": "2026-11-01T19:01:45Z", "updated_at": "2026-11-01T22:09:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Critical Modules and Biomarkers of Ulcerative Colitis by Using WGCNA.", "doi": "10.2147/JIR.S402715", "pmid": "37092131", "authors": ["Yifan Yuan", "Na Li", "Mingyue Fu", "Mei Ye"], "journal": "Journal of inflammation research", "year": 2023, "abstract": "Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and is characterized by relapsing and remitting episodes. We aimed to find biomarkers of UC and its causes.\nMethods: We got GSE73661 from the GEO database and used WGCNA to find DEGs that were expressed in the same way in both normal and UC samples. To identify the co-expression modules, we used Weighted Gene Co-Expression Network Analysis. Next, we selected genes that were both DEGs and parts of main modules. Later, three datasets were used to find the hub genes, and qRT-PCR was utilized to confirm the in-silico findings. Additionally, we analyzed the connection between the hub genes and the filtration of immune cells in UC. Using the databases, we made predictions about the miRNAs and lncRNAs that regulate the hub genes and predicted possible therapeutic drugs.\nResults: We found 822 DEGs and three main modules related to immunity, endoplasmic reticulum, and metabolism. Using another three datasets and human samples to confirm the mRNA expression of these genes in UC patients, XBP1 and PLPP1 were selected as hub genes, and had excellent diagnostic potential. According to the findings of the immune infiltration, patients with UC exhibited a larger proportion of immune cells. And hub genes, particularly XBP1, were closely linked to a number of immune cell infiltrations. Based on the databases and hub genes, a lncRNA-miRNA-mRNA network, including two miRNAs (miR-214-3p and miR-93-5p), two hub genes, and 124 lncRNAs, and potential therapeutic medicine were identified.\nConclusion: We found two new genes, XBP1 and PLPP1, that are involved in UC and can help diagnose and measure the disease. XBP1 also relates to clinical scores and immune cells. We suggested a gene network and possible drugs based on them.", "claims": [{"id": "claim-method", "statement": "Each candidate hub gene was tested using a receiver operating characteristic (ROC) curve to guarantee its precision.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37092131", "locator": "sections[9] \"Analysis of ROC Curves for Hub Genes\" paragraph 2", "quote": "Each candidate hub gene was tested using a receiver operating characteristic (ROC) curve to guarantee its precision."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). With a reasonable request, the corresponding author will provide access to the R code used in this work.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37092131", "locator": "sections[24] \"Data Sharing Statement\" paragraph 2", "quote": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). With a reasonable request, the corresponding author will provide access to the R code used in this work."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PLPP1 and XBP1 were identified as UC hub genes with strong diagnostic value, with area under the curve values of 0.986 and 0.991, respectively, and 0.994 for their combination.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37092131", "locator": "sections[17] \"Identification of Hub Genes and the Clinical Significance\" paragraph 2", "quote": "In GSE73661, the area under the curve for PLPP1, XBP1, and the combination were 0.986, 0.991, and 0.994 showing that the hub genes can function as UC biomarkers (Figure 5A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PLPP1 and XBP1 were identified as UC hub genes with strong diagnostic value, with area under the curve values of 0.986 and 0.991, respectively, and 0.994 for their combination.", "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:37092131"], "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:GSE11223"], "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:GSE11223"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37092131", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S402715", "sha256": "sha256:45db6f7e0bb37e21b27d27cea794164bb3e0b2a193324396a73d1865b1a1f397", "bytes": 34552, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S402715", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10120594", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11223", "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=GSE11223", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11223", "version": null, "note": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). With a reasonable request, the corresponding author will provide access to the R code used in this work.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). 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With a reasonable request, the corresponding author will provide access to the R code used in this work.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). 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With a reasonable request, the corresponding author will provide access to the R code used in this work.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). With a reasonable request, the corresponding author will provide access to the R code used in this work.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1187602", "GSM1187603", "GSM1187604", "GSM1187605", "GSM1187606", "GSM1187607", "GSM1187608", "GSM1187609", "GSM1187610", "GSM1187611", "GSM1187612", "GSM1187613", "GSM1187614", "GSM1187615", "GSM1187616", "GSM1187617", "GSM1187618", "GSM1187619", "GSM1187620", "GSM1187621", "GSM1187622"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (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": "data:geo:GSE73661", "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=GSE73661", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73661", "version": null, "note": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). With a reasonable request, the corresponding author will provide access to the R code used in this work.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All of the information utilized in this investigation may be found in the public domain at the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). 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