Exploring the pathogenesis of colorectal carcinoma complicated with hepatocellular carcinoma via microarray data analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37383715", "kind": "science-record", "revision": 4, "content_hash": "sha256:96f209b0fc01f1fec6068a753a2f21c82e267786002374431b02f2345a38bace", "created_at": "2026-11-01T19:02:08Z", "updated_at": "2026-11-01T22:52:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the pathogenesis of colorectal carcinoma complicated with hepatocellular carcinoma via microarray data analysis.", "doi": "10.3389/fphar.2023.1201401", "pmid": "37383715", "authors": ["Tianqi Gao", "Mengping Li", "Dailin Wu", "Ni Xiao", "Dan Huang", "Li Deng", "Lunwei Yang", "Chunhong Tian", "Yang Cao", "Jun Zhang", "Jihong Gu", "Yang Yu"], "journal": "Frontiers in pharmacology", "year": 2023, "abstract": "Background: Despite the increasing number of research endeavors dedicated to investigating the relationship between colorectal carcinoma (CRC) and hepatocellular carcinoma (HCC), the underlying pathogenic mechanism remains largely elusive. The aim of this study is to shed light on the molecular mechanism involved in the development of this comorbidity. Methods: The gene expression profiles of CRC (GSE90627) and HCC (GSE45267) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely, functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification, survival analysis and co-expression analysis. Results: A total of 150 common downregulated differentially expressed genes and 148 upregulated differentially expressed genes were selected for subsequent analyses. The significance of chemokines and cytokines in the pathogenesis of these two ailments is underscored by functional analysis. Seven gene modules that were closely connected were identified. Moreover, the lipopolysaccharide-mediated signaling pathway is intricately linked to the development of both diseases. Finally, 10 important hub genes were identified using cytoHubba, including CDK1, KIF11, CDC20, CCNA2, TOP2A, CCNB1, NUSAP1, BUB1B, ASPM, and MAD2L1. Conclusion: Our study reveals the common pathogenesis of colorectal carcinoma and hepatocellular carcinoma. These common pathways and hub genes may provide new ideas for further mechanism research.", "claims": [{"id": "claim-method", "statement": "We employed the GEOquery package to access the data and performed differential expression analysis using the Limma package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37383715", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "We employed the GEOquery package to access the data and performed differential expression analysis using the Limma package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE45267"], "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:GSE45267"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37383715", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fphar.2023.1201401", "sha256": "sha256:468bcf9c7bfca673e748a8ea232ee878a6c4ec81549ccbc246df16113e36bab1", "bytes": 43920, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fphar.2023.1201401", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10293624", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE45267", "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=GSE45267", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45267", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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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:37383715", "data:geo:GSE45267"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE45267"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:45:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13068, "completion_tokens": 1900, "cached_tokens": 264}}, "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:37383715", "type": "paper", "label": "pmid:37383715"}, {"id": "source:pmid:37383715", "type": "manuscript", "label": "PMID 37383715 full text"}, {"id": "data:geo:GSE45267", "type": "dataset", "label": "GEO GSE45267"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37383715", "type": "paper", "label": "pmid:37383715"}, {"id": "source:pmid:37383715", "type": "manuscript", "label": "PMID 37383715 full text"}, {"id": "data:geo:GSE45267", "type": "dataset", "label": "GEO GSE45267"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37383715", "type": "extraction", "used": ["source:pmid:37383715"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE45267", "type": "accession_resolution", "used": ["data:geo:GSE45267"], "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:37383715", "parent_hash": "sha256:0fc9dd25309ca721a8d69f2d4761227539ce6ad7e4e9c850bb35efae6800646e", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE45267 licence not read", "asset:data:geo:GSE45267 not downloaded", "asset:data:geo:GSE50579 licence not read", "asset:data:geo:GSE50579 not downloaded", "asset:data:geo:GSE89076 licence not read", "asset:data:geo:GSE89076 not downloaded", "asset:data:geo:GSE90627 licence not read", "asset:data:geo:GSE90627 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": ["omplicated with hepatocellular carcinoma via microarray data analysis."], "order_basis": "paper_text_order:52", "id": "assay:1"}, {"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": ["We employed the GEOquery package to access the data and performed differential expression analysis using the Limma package."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}