Identification of Hub Genes for Colorectal Cancer with Liver Metastasis Using miRNA-mRNA Network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36798788", "kind": "science-record", "revision": 3, "content_hash": "sha256:1d12bd26936c4b6a665f84a259e7906c47814540f33ac7b4bcdcbacf1a569630", "created_at": "2026-11-01T19:01:23Z", "updated_at": "2026-11-01T22:08:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes for Colorectal Cancer with Liver Metastasis Using miRNA-mRNA Network.", "doi": "10.1155/2023/2295788", "pmid": "36798788", "authors": ["Si-Ming Zhang", "Cheng Shen", "Jing Li", "Xing-Dan Wang", "Si-Qiu Zhai", "Ling-Ling Shi", "Dan-Li Lu", "Xiao-Hui Jiang", "Junlan Qiu"], "journal": "Disease markers", "year": 2023, "abstract": "Background: Liver metastasis is an important cause of death in patients with colorectal cancer (CRC). Increasing evidence indicates that microRNAs (miRNAs) are involved in the pathogenesis of colorectal cancer liver metastasis (CRLM). This study is aimed at exploring the potential miRNA-mRNA regulatory network.\nMethods: From the GEO database, we downloaded the microarray datasets GSE56350 and GSE73178. GEO2R was used to conduct differentially expressed miRNAs (DEMs) between CRC and CRLM using the GEO2R tool. Then, GO and KEGG pathway analysis for differentially expressed genes (DEGs) performed via DAVID. A protein-protein interaction (PPI) network was constructed by the STRING and identified by Cytoscape. Hub genes were identified by miRNA-mRNA network. Finally, the expression of the hub gene expression was assessed in the GSE81558.\nResults: The four DEMs (hsa-miR-204-5p, hsa-miR-122-5p, hsa-miR-95-3p, and hsa-miR-552-3p) were identified as common DEMs in GSE56350 and GSE73178 datasets. The SP1 was likely to adjust the upregulated DEMs; however, the YY1 could regulate both the upregulated and downregulated DEMs. A total of 3925 genes (3447 upregulated DEM genes and 478 downregulated DEM genes) were screened. These predicted genes were mainly linked to Platinum drug resistance, Cellular senescence, and ErbB signaling pathway. Through the gene network construction, most of the hub genes were found to be modulated by hsa-miR-204-5p, hsa-miR-122-5p, hsa-miR-95-3p, and hsa-miR-552-3p. Among the top 20 hub genes, the expression of CREB1, RHOA, and EGFR was significantly different in the GSE81558 dataset.\nConclusion: In this study, miRNA-mRNA networks in CRLM were screened between CRC patients and CRLM patients to provide a new method to predict for the pathogenesis and development of CRC.", "claims": [{"id": "claim-method", "statement": "DEMs between CRC and CRLM across different GEO datasets. |log2FC| > 1 and a P value of <0.05 are considered significantly by the GEO2R tool.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36798788", "locator": "sections[3] \"2.1. miRNA Microarray and DEG Identification\" paragraph 2", "quote": "DEMs between CRC and CRLM across different GEO datasets. |log2FC| > 1 and a P value of <0.05 are considered significantly by the GEO2R tool."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data were obtained from the public database described in Materials and Methods and carried out in accordance with relevant guidelines and regulations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36798788", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "All data were obtained from the public database described in Materials and Methods and carried out in accordance with relevant guidelines and regulations."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The four DEMs (hsa-miR-204-5p, hsa-miR-122-5p, hsa-miR-95-3p, and hsa-miR-552-3p) were identified as common DEMs in GSE56350 and GSE73178 datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36798788", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The four DEMs (hsa-miR-204-5p, hsa-miR-122-5p, hsa-miR-95-3p, and hsa-miR-552-3p) were identified as common DEMs in GSE56350 and GSE73178 datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The four DEMs (hsa-miR-204-5p, hsa-miR-122-5p, hsa-miR-95-3p, and hsa-miR-552-3p) were identified as common DEMs in GSE56350 and GSE73178 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:36798788"], "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:GSE56350"], "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:GSE56350"], "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:36798788", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2023/2295788", 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