Identification of Specific Biomarkers and Pathways in the Treatment Response of Infliximab for Inflammatory Bowel Disease: In-Silico Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36983834", "kind": "science-record", "revision": 4, "content_hash": "sha256:8e659fcc03d113fdd9891e738fd686439ba9cdb657a077292c634a1a20dfa6a1", "created_at": "2026-11-01T19:01:38Z", "updated_at": "2026-11-01T22:51:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Specific Biomarkers and Pathways in the Treatment Response of Infliximab for Inflammatory Bowel Disease: In-Silico Analysis.", "doi": "10.3390/life13030680", "pmid": "36983834", "authors": ["Rachid Kaddoura", "Hardik Ghelani", "Fatma Alqutami", "Hala Altaher", "Mahmood Hachim", "Reem Kais Jan"], "journal": "Life (Basel, Switzerland)", "year": 2023, "abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract. In biological therapy, infliximab became the first anti-tumor necrosis factor (TNF) agent approved for IBD. Despite this success, infliximab is expensive, often ineffective, and associated with adverse events. Prediction of infliximab resistance would improve overall potential outcomes. Therefore, there is a pressing need to widen the scope of investigating the role of genetics in IBD to their association with therapy response.\nMETHODS: In the current study, an in-silico analysis of publicly available IBD patient transcriptomics datasets from Gene Expression Omnibus (GEO) are used to identify subsets of differentially expressed genes (DEGs) involved in the pathogenesis of IBD and may serve as potential biomarkers for Infliximab response. Five datasets were found that met the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEOR2 tool. The probes' annotated genes in each dataset intersected with DGEs from all other datasets. Enriched gene Ontology Clustering for the identified genes was performed using Metascape to explore the possible connections or interactions between the genes.\nRESULTS: 174 DEGs between IBD and healthy controls were found from analyzing two datasets (GSE14580 and GSE73661), indicating a possible role in the pathogenesis of IBD. Of the 174 DEGs, five genes (SELE, TREM1, AQP9, FPR2, and HCAR3) were shared between all five datasets. Moreover, these five genes were identified as downregulated in the infliximab responder group compared to the non-responder group.\nCONCLUSIONS: We hypothesize that alteration in the expression of these genes leads to an impaired response to infliximab in IBD patients. Thus, these genes can serve as potential biomarkers for the early detection of compromised infliximab response in IBD patients.", "claims": [{"id": "claim-method", "statement": "The ‘limma’ package was used for the statistical analysis of DEGs and for applying precision weights. Statistical analysis was carried out using the ‘ebayes’ function from the ‘limma’ package, and all outputs were exported.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36983834", "locator": "sections[4] \"2.2. Identification of Common DEGs and Pathway Enrichment Analysis\" paragraph 2", "quote": "The ‘limma’ package was used for the statistical analysis of DEGs and for applying precision weights. Statistical analysis was carried out using the ‘ebayes’ function from the ‘limma’ package, and all outputs were exported."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36983834", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Of the 174 DEGs, five genes (SELE, TREM1, AQP9, FPR2, and HCAR3) were shared between all five datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36983834", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Of the 174 DEGs, five genes (SELE, TREM1, AQP9, FPR2, and HCAR3) were shared between all five datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Of the 174 DEGs, five genes (SELE, TREM1, AQP9, FPR2, and HCAR3) were shared between all five datasets.", "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:36983834"], "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:GSE111761"], "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:GSE111761"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36983834", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/life13030680", "sha256": "sha256:4c07de24f2a846dceab04850cbbbf614900f415ac30ea2a905abf94f366ba623", "bytes": 28196, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/life13030680", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10057676", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE111761", "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=GSE111761", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE111761", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3039427", "GSM3039428", "GSM3039429", "GSM3039430", "GSM3039431", "GSM3039432"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "13497", "taxon": "Homo sapiens", "title": "Differential expression of IBD susceptibility and IL23R associated pathway genes during ongoing anti-TNF therapy (anti-TNF non-responder vs anti-TNF responder)", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"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 analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "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:GSE14580", "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=GSE14580", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14580", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM364627", "GSM364628", "GSM364629", "GSM364630", "GSM364631", "GSM364632", "GSM364633", "GSM364634", "GSM364635", "GSM364636", "GSM364637", "GSM364638", "GSM364639", "GSM364640", "GSM364641", "GSM364642", "GSM364643", "GSM364644", "GSM364645", "GSM364646", "GSM364647", "GSM364648", "GSM364649", "GSM364650", "GSM364651", "GSM364652", "GSM364653", "GSM364654", "GSM364655", "GSM364656"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Mucosal gene signatures to predict response to infliximab in patients with 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:GSE23597", "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=GSE23597", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23597", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM578713", "GSM578714", "GSM578715", "GSM578716", "GSM578717", "GSM578718", "GSM578719", "GSM578720", "GSM578721", "GSM578722", "GSM578723", "GSM578724", "GSM578725", "GSM578726", "GSM578727", "GSM578728", "GSM578729", "GSM578730", "GSM578731", "GSM578732", "GSM578733", "GSM578734", "GSM578735", "GSM578736", "GSM578737", "GSM578738", "GSM578739", "GSM578740", "GSM578741", "GSM578742", "GSM578743", "GSM578744", "GSM578745", "GSM578746", "GSM578747", "GSM578748", "GSM578749", "GSM578750", "GSM578751", "GSM578752", "GSM578753", "GSM578754", "GSM578755", "GSM578756", "GSM578757", "GSM578758", "GSM578759", "GSM578760", "GSM578761", "GSM578762", "GSM578763", "GSM578764", "GSM578765", "GSM578766", "GSM578767", "GSM578768", "GSM578769", "GSM578770", "GSM578771", "GSM578772", "GSM578773", "GSM578774", "GSM578775", "GSM578776", "GSM578777", "GSM578778", "GSM578779", "GSM578780", "GSM578781", "GSM578782", "GSM578783", "GSM578784", "GSM578785", "GSM578786", "GSM578787", "GSM578788", "GSM578789", "GSM578790", "GSM578791", "GSM578792", "GSM578793", "GSM578794", "GSM578795", "GSM578796", "GSM578797", "GSM578798", "GSM578799", "GSM578800", "GSM578801", "GSM578802", "GSM578803", "GSM578804", "GSM578805", "GSM578806", "GSM578807", "GSM578808", "GSM578809", "GSM578810", "GSM578811", "GSM578812", "GSM578813", "GSM578814", "GSM578815", "GSM578816", "GSM578817", "GSM578818", "GSM578819", "GSM578820", "GSM578821", "GSM578822", "GSM578823", "GSM578824", "GSM578825"], "sample_count": 113, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from colonic biopsy samples of infliximab treated UC patients", "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: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": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1900148", "GSM1900149", "GSM1900150", "GSM1900151", "GSM1900152", "GSM1900153", "GSM1900154", "GSM1900155", "GSM1900156", "GSM1900157", "GSM1900158", "GSM1900159", "GSM1900160", "GSM1900161", "GSM1900162", "GSM1900163", "GSM1900164", "GSM1900165", "GSM1900166", "GSM1900167", "GSM1900168", "GSM1900169", "GSM1900170", "GSM1900171", "GSM1900172", "GSM1900173", "GSM1900174", "GSM1900175", "GSM1900176", "GSM1900177", "GSM1900178", "GSM1900179", "GSM1900180", "GSM1900181", "GSM1900182", "GSM1900183", "GSM1900184", "GSM1900185", "GSM1900186", "GSM1900187", "GSM1900188", "GSM1900189", "GSM1900190", "GSM1900191", "GSM1900192", "GSM1900193", "GSM1900194", "GSM1900195", "GSM1900196", "GSM1900197", "GSM1900198", "GSM1900199", "GSM1900200", "GSM1900201", "GSM1900202", "GSM1900203", "GSM1900204", "GSM1900205", "GSM1900206", "GSM1900207", "GSM1900208", "GSM1900209", "GSM1900210", "GSM1900211", "GSM1900212", "GSM1900213", "GSM1900214", "GSM1900215", "GSM1900216", "GSM1900217", "GSM1900218", "GSM1900219", "GSM1900220", "GSM1900221", "GSM1900222", "GSM1900223", "GSM1900224", "GSM1900225", "GSM1900226", "GSM1900227", "GSM1900228", "GSM1900229", "GSM1900230", "GSM1900231", "GSM1900232", "GSM1900233", "GSM1900234", "GSM1900235", "GSM1900236", "GSM1900237", "GSM1900238", "GSM1900239", "GSM1900240", "GSM1900241", "GSM1900242", "GSM1900243", "GSM1900244", "GSM1900245", "GSM1900246", "GSM1900247", "GSM1900248", "GSM1900249", "GSM1900250", "GSM1900251", "GSM1900252", "GSM1900253", "GSM1900254", "GSM1900255", "GSM1900256", "GSM1900257", "GSM1900258", "GSM1900259", "GSM1900260", "GSM1900261", "GSM1900262", "GSM1900263", "GSM1900264", "GSM1900265", "GSM1900266", "GSM1900267", "GSM1900268", "GSM1900269", "GSM1900270", "GSM1900271", "GSM1900272", "GSM1900273", "GSM1900274", "GSM1900275", "GSM1900276", "GSM1900277", "GSM1900278", "GSM1900279", "GSM1900280", "GSM1900281", "GSM1900282", "GSM1900283", "GSM1900284", "GSM1900285", "GSM1900286", "GSM1900287", "GSM1900288", "GSM1900289", "GSM1900290", "GSM1900291", "GSM1900292", "GSM1900293", "GSM1900294", "GSM1900295", "GSM1900296", "GSM1900297", "GSM1900298", "GSM1900299", "GSM1900300", "GSM1900301", "GSM1900302", "GSM1900303", "GSM1900304", "GSM1900305", "GSM1900306", "GSM1900307", "GSM1900308", "GSM1900309", "GSM1900310", "GSM1900311", "GSM1900312", "GSM1900313", "GSM1900314", "GSM1900315", "GSM1900316", "GSM1900317", "GSM1900318", "GSM1900319", "GSM1900320", "GSM1900321", "GSM1900322", "GSM1900323", "GSM1900324", "GSM1900325"], "sample_count": 178, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "The effect of vedolizumab (anti-α4β7-integrin) therapy on colonic mucosal gene expression in patients with ulcerative colitis (UC)", "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:GSE111761 not downloaded", "asset:data:geo:GSE111761 licence not read", "asset:data:geo:GSE12251 not downloaded", "asset:data:geo:GSE12251 licence not read", "asset:data:geo:GSE14580 not downloaded", "asset:data:geo:GSE14580 licence not read", "asset:data:geo:GSE23597 not downloaded", "asset:data:geo:GSE23597 licence not read", "asset:data:geo:GSE73661 not downloaded", "asset:data:geo:GSE73661 licence not read"]}, "analysis": {"state": "partial", "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": "The ‘limma’ package was used for the statistical analysis of DEGs and for applying precision weights. Statistical analysis was carried out using the ‘ebayes’ function from the ‘limma’ package, and all outputs were exported."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "student t-test"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE14580", "GSE73661", "GSE12251", "GSE23597", "GSE111761"], "resolved_accessions": ["GSE14580", "GSE73661", "GSE12251", "GSE23597", "GSE111761"], "statements": ["The datasets analyzed during the current study are available in the Gene Expression Omnibus repository, https://www.ncbi.nlm.nih.gov/geo/, accessed on 15 November 2022. Individual dataset link is provided below: Accession No. GSE14580, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580; Accession No. GSE73661, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73661; Accession No. GSE12251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12251; Accession No. GSE23597, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23597; Accession No. GSE111761, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111761."], "basis": "The paper names GSE14580, GSE73661, GSE12251, GSE23597, GSE111761 in Gene Expression Omnibus repository 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:36983834", "data:geo:GSE111761"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE111761"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:35:12Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8226, "completion_tokens": 2345, "cached_tokens": 128}}, "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:36983834", "type": "paper", "label": "pmid:36983834"}, {"id": "source:pmid:36983834", "type": "manuscript", "label": "PMID 36983834 full text"}, {"id": "data:geo:GSE111761", "type": "dataset", "label": "GEO GSE111761"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36983834", "type": "paper", "label": "pmid:36983834"}, {"id": "source:pmid:36983834", "type": "manuscript", "label": "PMID 36983834 full text"}, {"id": "data:geo:GSE111761", "type": "dataset", "label": "GEO GSE111761"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36983834", "type": "extraction", "used": ["source:pmid:36983834"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE111761", "type": "accession_resolution", "used": ["data:geo:GSE111761"], "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:36983834", "parent_hash": "sha256:f34a4d67f5612419f18d1feab0e69034c76a78ab03f551b4f53a8827ca734a41", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE111761 licence not read", "asset:data:geo:GSE111761 not downloaded", "asset:data:geo:GSE12251 licence not read", "asset:data:geo:GSE12251 not downloaded", "asset:data:geo:GSE14580 licence not read", "asset:data:geo:GSE14580 not downloaded", "asset:data:geo:GSE23597 licence not read", "asset:data:geo:GSE23597 not downloaded", "asset:data:geo:GSE73661 licence not read", "asset:data:geo:GSE73661 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": ["The ‘limma’ package was used for the statistical analysis of DEGs and for applying precision weights. Statistical analysis was carried out using the ‘ebayes’ function from the ‘limma’ package, and all outputs were exported."], "order_basis": "analysis_only", "id": "assay:1"}]}