The molecular basis of the associations between non-alcoholic fatty liver disease and colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36568397", "kind": "science-record", "revision": 4, "content_hash": "sha256:4d0e1a0bbb4707e8cc81294493f9267c868be125bab91eb4bf7e8ad073b8767a", "created_at": "2026-11-01T19:01:07Z", "updated_at": "2026-11-01T22:50:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The molecular basis of the associations between non-alcoholic fatty liver disease and colorectal cancer.", "doi": "10.3389/fgene.2022.1007337", "pmid": "36568397", "authors": ["Ting Qiu", "Weitao Hu", "Zilan Rao", "Taiyong Fang"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: Given the ongoing research on non-alcoholic fatty liver disease (NAFLD) and colorectal cancer (CRC), the number of studies suggesting a strong link between NAFLD and CRC is on the rise, while its underlying pathological mechanisms remain uncertain. This study aims to explore the shared genes and mechanisms and to reveal the molecular basis of the association between CRC and NAFLD through bioinformatics approaches. Methods: The Gene Expression Omnibus (GEO) dataset GSE89632 is downloaded for NAFLD cases and healthy controls. Additionally, the GSE4107 and GSE9348 datasets are obtained for CRC cases and healthy controls. Differentially expressed genes (DEGs) are obtained for NAFLD and CRC datasets, as well as shared genes between the two disorders. GO and KEGG enrichment analyses are further conducted. Subsequently, the STRING database and Cytoscape software are utilized to establish the PPI network and identify the hub genes. Then, co-expression analysis is performed using GeneMANIA. Subsequently, ROC curves and external datasets validation were applied to further screen the candidate markers. Finally, NetworkAnalyst is available as a means to construct a miRNA-gene regulatory network. Results: Under the threshold of FDR ≤ 0.01, 147 common genes are obtained in NAFLD and CRC. Categorization of GO functions shows that DEGs are predominantly enriched in \"response to organic substance\", \"cellular response to chemical stimulus\", and \"response to external stimulus\". The predominant KEGG pathways in DEGs are the \"IL-17 signaling pathway\", the \"TNF signaling pathway\", \"Viral protein interaction with cytokine and cytokine receptor\", \"Cytokine-cytokine receptor interaction\", and the \"Toll-like receptor signaling pathway\". Additionally, MYC, IL1B, FOS, CXCL8, PTGS2, MMP9, JUN, and IL6 are identified as hub genes by the evaluation of 7 algorithms. With the construction of miRNA-gene networks, 2 miRNAs, including miR-106a-5p, and miR-204-5p are predicted to be potential key miRNAs. Conclusion: This study identifies possible hub genes acting in the co-morbidity of NAFLD and CRC and discovers the interaction of miRNAs and hub genes, providing a novel understanding of the molecular basis for the relevance of CRC and NAFLD, thus contributing to the development of new therapeutic strategies to combat NAFLD and CRC.", "claims": [{"id": "claim-method", "statement": "The “limma” package from R software is used to identify the differentially expressed genes (DEGs) in the NAFLD and CRC datasets respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36568397", "locator": "sections[4] \"Differentially expressed genes selection\" paragraph 2", "quote": "The “limma” package from R software is used to identify the differentially expressed genes (DEGs) in the NAFLD and CRC datasets respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36568397", "locator": "sections[18] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Under an FDR threshold of 0.01, 147 common genes were obtained in NAFLD and CRC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36568397", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Under the threshold of FDR ≤ 0.01, 147 common genes are obtained in NAFLD and CRC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Under an FDR threshold of 0.01, 147 common genes were obtained in NAFLD and CRC.", "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:36568397"], "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:GSE163211"], "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:GSE163211"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36568397", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.1007337", "sha256": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36568397", "data:geo:GSE163211"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE163211"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:21:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8597, "completion_tokens": 1544, "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:36568397", "type": "paper", "label": "pmid:36568397"}, {"id": "source:pmid:36568397", "type": "manuscript", "label": "PMID 36568397 full text"}, {"id": "data:geo:GSE163211", "type": "dataset", "label": "GEO GSE163211"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36568397", "type": "paper", "label": "pmid:36568397"}, {"id": "source:pmid:36568397", "type": "manuscript", "label": "PMID 36568397 full text"}, {"id": "data:geo:GSE163211", "type": "dataset", "label": "GEO GSE163211"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36568397", "type": "extraction", "used": ["source:pmid:36568397"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE163211", "type": "accession_resolution", "used": ["data:geo:GSE163211"], "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:36568397", "parent_hash": "sha256:65dcd455b05f044647319ec76614c40cec62ce04ea67958825b536bffedd7428", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE163211 licence not read", "asset:data:geo:GSE163211 not downloaded", "asset:data:geo:GSE184093 licence not read", "asset:data:geo:GSE184093 not downloaded", "asset:data:geo:GSE4107 licence not read", "asset:data:geo:GSE4107 not downloaded", "asset:data:geo:GSE89632 licence not read", "asset:data:geo:GSE89632 not downloaded", "asset:data:geo:GSE9348 licence not read", "asset:data:geo:GSE9348 not downloaded", "execution.not_run", "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 from R software is used to identify the differentially expressed genes (DEGs) in the NAFLD and CRC datasets respectively."], "order_basis": "analysis_only", "id": "assay:1"}]}