Cross talk between bacterial and human gene networks enriched using ncRNAs in IBD disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37169818", "kind": "science-record", "revision": 4, "content_hash": "sha256:599be16e234307881e71ed025572fe7038018370d2b781e9c26c125f9000c88d", "created_at": "2026-11-01T19:01:50Z", "updated_at": "2026-11-01T22:51:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Cross talk between bacterial and human gene networks enriched using ncRNAs in IBD disease.", "doi": "10.1038/s41598-023-34780-x", "pmid": "37169818", "authors": ["Mohammad Elahimanesh", "Mohammad Najafi"], "journal": "Scientific reports", "year": 2023, "abstract": "Inflammatory bowel disease (IBD) is a long-term inflammatory immune-mediated gut illness with several extra-intestinal complications. The aims of this study were to identify a novel network-based meta-analysis approach on the basis of the combinations of the differentially expressed genes (DEGs) from microarray data, to enrich the functional modules from human protein-protein interaction (PPI) and gene ontology (GO) data, and to profile the ncRNAs on the genes involved in IBD. The gene expression profiles of GSE126124, GSE87473, GSE75214, and GSE95095 are obtained from the Gene Expression Omnibus (GEO) database based on the study criteria between 2017 and 2022. The DEGs were screened by the R software. DEGs were then used to examine gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The ncRNAs including the miRNAs and ceRNAs were predicted on the PPIs visualized using Cytoscape. Enrichment analysis of genes with differential expression (n = 342) using KEGG and GO showed that the signaling pathways related with staphylococcus aureus and pertussis bacterial infections may stimulate the immune system and exacerbate IBD via the interaction with human proteins including Fibrinogen gamma chain (FGG), Keratin 10 (KRT10), and Toll like receptor 4 (TLR4). By building a ceRNA network, lncRNA XIST and NEAT1 were determined by affecting common miRNAs, hsa-miR-6875-5p, hsa-miR-1908-5p, hsa-miR-186-5p, hsa-miR-6763-5p, hsa-miR-4436a, and hsa-miR-520a-5p. Additionally, the chromosome regions including NM_001039703 and NM_006267, which produce the most potent circRNAs play a significant role in the ceRNA network of IBD. Also, we predicted the siRNAs that would be most effective against the bacterial genes in staphylococcus aureus and pertussis infections. These findings suggested that three genes (FGG, KRT10, and TLR4), six miRNAs (hsa-miR-6875-5p, hsa-miR-1908-5p, hsa-miR-186-5p, hsa-miR-4436a, hsa-miR-520a-5p, and hsa-miR-6763-5p), two lncRNAs (XIST and NEAT1), and chromosomal regions including NM_001039703 and NM_006267 with the production of the most effective circRNAs are involved in the ncRNA-associated ceRNA network of IBD. These ncRNA profiles are related to the described gene functions and may play therapeutic targets in controlling inflammatory bowel disease.", "claims": [{"id": "claim-method", "statement": "Using the LIMMA package36, Student's t-test was done and genes with differential expression levels between the two groups of controls and IBD patients were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37169818", "locator": "sections[8] \"Statistical analysis and data-processing\" paragraph 2", "quote": "Using the LIMMA package36, Student's t-test was done and genes with differential expression levels between the two groups of controls and IBD patients were identified."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37169818", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 342 differentially expressed genes were identified between IBD and control samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37169818", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Enrichment analysis of genes with differential expression (n = 342) using KEGG and GO showed that the signaling pathways related with staphylococcus aureus and pertussis bacterial infections may stimulate the immune system and exacerbate IBD via the interaction with human proteins including Fibrinogen gamma chain (FGG), Keratin 10 (KRT10), and Toll like receptor 4 (TLR4)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 342 differentially expressed genes were identified between IBD and control samples.", "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:37169818"], "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:GSE126124"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE126124"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37169818", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-34780-x", "sha256": "sha256:e3e93296fdda197e48669302c43e984bf08783cb5c54fa336286cbd75feea5a0", "bytes": 37165, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-34780-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10175251", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE126124", "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=GSE126124", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE126124", "version": null, "note": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3591886", "GSM3591887", "GSM3591888", "GSM3591889", "GSM3591890", "GSM3591891", "GSM3591892", "GSM3591893", "GSM3591894", "GSM3591895", "GSM3591896", "GSM3591897", "GSM3591898", "GSM3591899", "GSM3591900", "GSM3591901", "GSM3591902", "GSM3591903", "GSM3591904", "GSM3591905", "GSM3591906", "GSM3591907", "GSM3591908", "GSM3591909", "GSM3591910", "GSM3591911", "GSM3591912", "GSM3591913", "GSM3591914", "GSM3591915", "GSM3591916", "GSM3591917", "GSM3591918", "GSM3591919", "GSM3591920", "GSM3591921", "GSM3591922", "GSM3591923", "GSM3591924", "GSM3591925", "GSM3591926", "GSM3591927", "GSM3591928", "GSM3591929", "GSM3591930", "GSM3591931", "GSM3591932", "GSM3591933", "GSM3591934", "GSM3591935", "GSM3591936", "GSM3591937", "GSM3591938", "GSM3591939", "GSM3591940", "GSM3591941", "GSM3591942", "GSM3591943", "GSM3591944", "GSM3591945", "GSM3591946", "GSM3591947", "GSM3591948", "GSM3591949", "GSM3591950", "GSM3591951", "GSM3591952", "GSM3591953", "GSM3591954", "GSM3591955", "GSM3591956", "GSM3591957", "GSM3591958", "GSM3591959", "GSM3591960", "GSM3591961", "GSM3591962", "GSM3591963", "GSM3591964", "GSM3591965", "GSM3591966", "GSM3591967", "GSM3591968", "GSM3591969", "GSM3591970", "GSM3591971", "GSM3591972", "GSM3591973", "GSM3591974", "GSM3591975", "GSM3591976", "GSM3591977", "GSM3591978", "GSM3591979", "GSM3591980", "GSM3591981", "GSM3591982", "GSM3591983", "GSM3591984", "GSM3591985", "GSM3591986", "GSM3591987", "GSM3591988", "GSM3591989", "GSM3591990", "GSM3591991", "GSM3591992", "GSM3591993", "GSM3591994", "GSM3591995", "GSM3591996", "GSM3591997", "GSM3591998", "GSM3591999", "GSM3592000", "GSM3592001", "GSM3592002", "GSM3592003", "GSM3592004", "GSM3592005", "GSM3592006", "GSM3592007", "GSM3592008", "GSM3592009", "GSM3592010", "GSM3592011", "GSM3592012", "GSM3592013", "GSM3592014", "GSM3592015", "GSM3592016", "GSM3592017", "GSM3592018", "GSM3592019", "GSM3592020", "GSM3592021", "GSM3592022", "GSM3592023", "GSM3592024", "GSM3592025", "GSM3592026", "GSM3592027", "GSM3592028", "GSM3592029", "GSM3592030", "GSM3592031", "GSM3592032", "GSM3592033", "GSM3592034", "GSM3592035", "GSM3592036", "GSM3592037", "GSM3592038", "GSM3592039", "GSM3592040", "GSM3592041", "GSM3592042", "GSM3592043", "GSM3592044", "GSM3592045", "GSM3592046", "GSM3592047", "GSM3592048", "GSM3592049", "GSM3592050", "GSM3592051", "GSM3592052", "GSM3592053", "GSM3592054", "GSM3592055", "GSM3592056", "GSM3592057", "GSM3592058", "GSM3592059", "GSM3592060", "GSM3592061"], "sample_count": 176, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.", "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:GSE75214", "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=GSE75214", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75214", "version": null, "note": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1426071", "GSM1426072", "GSM1426073", "GSM1426074", "GSM1426075", "GSM1426076", "GSM1426077", "GSM1426078", "GSM1426079", "GSM1426080", "GSM1426081", "GSM1426082", "GSM1426083", "GSM1426084", "GSM1426085", "GSM1426086", "GSM1426087", "GSM1426088", "GSM1426089", "GSM1426090", "GSM1426091", "GSM1426092", "GSM1426093", "GSM1426094", "GSM1426095", "GSM1426096", "GSM1426097", "GSM1426098", "GSM1426099", "GSM1426100", "GSM1426101", "GSM1426102", "GSM1426103", "GSM1426104", "GSM1426105", "GSM1426106", "GSM1426107", "GSM1426108", "GSM1426109", "GSM1426110", "GSM1426111", "GSM1426112", "GSM1426113", "GSM1426114", "GSM1426115", "GSM1426116", "GSM1426117", "GSM1426118", "GSM1426119", "GSM1426120", "GSM1426121", "GSM1426122", "GSM1426123", "GSM1426124", "GSM1426125", "GSM1426126", "GSM1426127", "GSM1426128", "GSM1426129", "GSM1426130", "GSM1426131", "GSM1426132", "GSM1426133", "GSM1426134", "GSM1426135", "GSM1426136", "GSM1426137", "GSM1426138", "GSM1426139", "GSM1426140", "GSM1426141", "GSM1426142", "GSM1426143", "GSM1426144", "GSM1426145", "GSM1426146", "GSM1426147", "GSM1426148", "GSM1426149", "GSM1426150", "GSM1426151", "GSM1426152", "GSM1426153", "GSM1426154", "GSM1426155", "GSM1426156", "GSM1426157", "GSM1426158", "GSM1426159", "GSM1426160", "GSM1426161", "GSM1426162", "GSM1426163", "GSM1426164", "GSM1426165", "GSM1426166", "GSM1426167", "GSM1426168", "GSM1426169", "GSM1426170", "GSM1426171", "GSM1426172", "GSM1426173", "GSM1426174", "GSM1426175", "GSM1426176", "GSM1426177", "GSM1426178", "GSM1426179", "GSM1426180", "GSM1426181", "GSM1426182", "GSM1426183", "GSM1426184", "GSM1426185", "GSM1426186", "GSM1945759", "GSM1945760", "GSM1945761", "GSM1945762", "GSM1945763", "GSM1945764", "GSM1945765", "GSM1945766", "GSM1945767", "GSM1945768", "GSM1945769", "GSM1945770", "GSM1945771", "GSM1945772", "GSM1945773", "GSM1945774", "GSM1945775", "GSM1945776", "GSM1945777", "GSM1945778", "GSM1945779", "GSM1945780", "GSM1945781", "GSM1945782", "GSM1945783", "GSM1945784", "GSM1945785", "GSM1945786", "GSM1945787", "GSM1945788", "GSM1945789", "GSM1945790", "GSM1945791", "GSM1945792", "GSM1945793", "GSM1945794", "GSM1945795", "GSM1945796", "GSM1945797", "GSM1945798", "GSM1945799", "GSM1945800", "GSM1945801", "GSM1945802", "GSM1945803", "GSM1945804", "GSM1945805", "GSM1945806", "GSM1945807", "GSM1945808", "GSM1945809", "GSM1945810", "GSM1945811", "GSM1945812", "GSM1945813", "GSM1945814", "GSM1945815", "GSM1945816", "GSM1945817", "GSM1945818", "GSM1945819", "GSM1945820", "GSM1945821", "GSM1945822", "GSM1945823", "GSM1945824", "GSM1945825", "GSM1945826", "GSM1945827", "GSM1945828", "GSM1945829", "GSM1945830", "GSM1945831", "GSM1945832", "GSM1945833", "GSM1945834", "GSM1945835", "GSM1945836"], "sample_count": 194, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in patients with inflammatory bowel disease study", "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:GSE87473", "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=GSE87473", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87473", "version": null, "note": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2332079", "GSM2332080", "GSM2332081", "GSM2332082", "GSM2332083", "GSM2332084", "GSM2332085", "GSM2332086", "GSM2332087", "GSM2332088", "GSM2332089", "GSM2332090", "GSM2332091", "GSM2332092", "GSM2332093", "GSM2332094", "GSM2332095", "GSM2332096", "GSM2332097", "GSM2332098", "GSM2332099", "GSM2332100", "GSM2332101", "GSM2332102", "GSM2332103", "GSM2332104", "GSM2332105", "GSM2332106", "GSM2332107", "GSM2332108", "GSM2332109", "GSM2332110", "GSM2332111", "GSM2332112", "GSM2332113", "GSM2332114", "GSM2332115", "GSM2332116", "GSM2332117", "GSM2332118", "GSM2332119", "GSM2332120", "GSM2332121", "GSM2332122", "GSM2332123", "GSM2332124", "GSM2332125", "GSM2332126", "GSM2332127", "GSM2332128", "GSM2332129", "GSM2332130", "GSM2332131", "GSM2332132", "GSM2332133", "GSM2332134", "GSM2332135", "GSM2332136", "GSM2332137", "GSM2332138", "GSM2332139", "GSM2332140", "GSM2332141", "GSM2332142", "GSM2332143", "GSM2332144", "GSM2332145", "GSM2332146", "GSM2332147", "GSM2332148", "GSM2332149", "GSM2332150", "GSM2332151", "GSM2332152", "GSM2332153", "GSM2332154", "GSM2332155", "GSM2332156", "GSM2332157", "GSM2332158", "GSM2332159", "GSM2332160", "GSM2332161", "GSM2332162", "GSM2332163", "GSM2332164", "GSM2332165", "GSM2332166", "GSM2332167", "GSM2332168", "GSM2332169", "GSM2332170", "GSM2332171", "GSM2332172", "GSM2332173", "GSM2332174", "GSM2332175", "GSM2332176", "GSM2332177", "GSM2332178", "GSM2332179", "GSM2332180", "GSM2332181", "GSM2332182", "GSM2332183", "GSM2332184", "GSM2332185", "GSM2332186", "GSM2332187", "GSM2332188", "GSM2332189", "GSM2332190", "GSM2332191", "GSM2332192", "GSM2332193", "GSM2332194", "GSM2332195", "GSM2332196", "GSM2332197", "GSM2332198", "GSM2332199", "GSM2332200", "GSM2332201", "GSM2332202", "GSM2332203", "GSM2332204", "GSM2332205"], "sample_count": 127, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Gene expression profiling of mucosal biopsies from pediatric or adult patients with moderately to severely active ulcerative colitis", "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:GSE95095", "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=GSE95095", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95095", "version": null, "note": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2496058", "GSM2496059", "GSM2496060", "GSM2496061", "GSM2496062", "GSM2496063", "GSM2496064", "GSM2496065", "GSM2496066", "GSM2496067", "GSM2496068", "GSM2496069", "GSM2496070", "GSM2496071", "GSM2496072", "GSM2496073", "GSM2496074", "GSM2496075", "GSM2496076", "GSM2496077", "GSM2496078", "GSM2496079", "GSM2496080", "GSM2496081", "GSM2496082", "GSM2496083", "GSM2496084", "GSM2496085", "GSM2496086", "GSM2496087", "GSM2496088", "GSM2496089", "GSM2496090", "GSM2496091", "GSM2496092", "GSM2496093", "GSM2496094", "GSM2496095", "GSM2496096", "GSM2496097", "GSM2496098", "GSM2496099", "GSM2496100", "GSM2496101", "GSM2496102", "GSM2496103", "GSM2496104", "GSM2496105", "GSM2496106", "GSM2496107", "GSM2496108", "GSM2496109", "GSM2496110", "GSM2496111", "GSM2496112", "GSM2496113", "GSM2496114", "GSM2496115", "GSM2496116", "GSM2496117"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Differential Gene Expression between involved and uninvolved sites of Crohn’s disease: Insights into a Distinctive Pathogenesis Profile", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE126124 not downloaded", "asset:data:geo:GSE126124 licence not read", "asset:data:geo:GSE75214 not downloaded", "asset:data:geo:GSE75214 licence not read", "asset:data:geo:GSE87473 not downloaded", "asset:data:geo:GSE87473 licence not read", "asset:data:geo:GSE95095 not downloaded", "asset:data:geo:GSE95095 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Using the LIMMA package36, Student's t-test was done and genes with differential expression levels between the two groups of controls and IBD patients were identified."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "LIMMA"}}, {"id": "method-3", "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"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE126124", "GSE87473", "GSE75214", "GSE95095"], "resolved_accessions": ["GSE126124", "GSE87473", "GSE75214", "GSE95095"], "statements": ["The datasets (GSE126124, GSE87473, GSE75214, and GSE95095) used during the current study are available from NCBI, GEO (https://www.ncbi.nlm.nih.gov/geo/). However, other data analyzed in the article can present by the corresponding author on reasonable request."], "basis": "The paper names GSE126124, GSE87473, GSE75214, GSE95095 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": [], "assets": ["source:pmid:37169818", "data:geo:GSE126124"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE126124"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:39:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10286, "completion_tokens": 1907, "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:37169818", "type": "paper", "label": "pmid:37169818"}, {"id": "source:pmid:37169818", "type": "manuscript", "label": "PMID 37169818 full text"}, {"id": "data:geo:GSE126124", "type": "dataset", "label": "GEO GSE126124"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37169818", "type": "paper", "label": "pmid:37169818"}, {"id": "source:pmid:37169818", "type": "manuscript", "label": "PMID 37169818 full text"}, {"id": "data:geo:GSE126124", "type": "dataset", "label": "GEO GSE126124"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37169818", "type": "extraction", "used": ["source:pmid:37169818"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE126124", "type": "accession_resolution", "used": ["data:geo:GSE126124"], "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:37169818", "parent_hash": "sha256:f2e1182c119d3bd995a150cb735bf50d7c1e9ce47db34af1e460c6554a37ae8f", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE126124 licence not read", "asset:data:geo:GSE126124 not downloaded", "asset:data:geo:GSE75214 licence not read", "asset:data:geo:GSE75214 not downloaded", "asset:data:geo:GSE87473 licence not read", "asset:data:geo:GSE87473 not downloaded", "asset:data:geo:GSE95095 licence not read", "asset:data:geo:GSE95095 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["e differentially expressed genes (DEGs) from microarray data, to enrich the functional modules from"], "order_basis": "paper_text_order:348", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Using the LIMMA package36, Student's t-test was done and genes with differential expression levels between the two groups of controls and IBD patients were identified."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}