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pmid:30807603
Development of novel predictive miRNA/target gene pathways for colorectal cancer distance metastasis to the liver using a bioinformatic approach.
Precious Takondwa Makondi · Po-Li Wei · Chien-Yu Huang · Yu-Jia Chang
PloS one · 2019 doi:10.1371/journal.pone.0211968
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Experiment
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Data
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Analysis
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Execution
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30807603", "kind": "science-record", "revision": 7, "content_hash": "sha256:d49da47189eaca6555b7f655ce7a30d5b2b16dc52f4ff12a9e0b74ce8640ee70", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:00:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of novel predictive miRNA/target gene pathways for colorectal cancer distance metastasis to the liver using a bioinformatic approach.", "doi": "10.1371/journal.pone.0211968", "pmid": "30807603", "authors": ["Precious Takondwa Makondi", "Po-Li Wei", "Chien-Yu Huang", "Yu-Jia Chang"], "journal": "PloS one", "year": 2019, "abstract": "BACKGROUND: Liver metastases are the major cause of colorectal cancer (CRC)-related deaths. However, there is no reliable clinical predictor for CRC progression to liver metastasis. In this study, we investigated possible predictors (miRNAs and biomarkers) for clinical application.\nMETHODOLOGY: The Gene Expression Omnibus (GEO) datasets GSE49355, GSE41258 and GSE81558 for genes and GSE54088 and GSE56350 for miRNAs were used to identify common differentially expressed genes (DEGs) and miRNAs between primary CRC tissues and liver metastases. The identified miRNAs and their targets from the DEGs were verified in datasets comprising gene, miRNA and miRNA exosome profiles of CRC patients with no distant metastases (M0) and distant metastases (M1); the interaction networks and pathways were also mapped.\nRESULTS: There were 49 upregulated and 13 downregulated DEGs and 16 downregulated and 14 upregulated miRNAs; between the DEGs and miRNA targets, there were five upregulated and four downregulated genes. MiR-20a was strongly correlated with the status of liver metastasis. MiR-20a, miR499a, and miR-576-5p were highly correlated with the metastatic outcomes. MiR-20a was significantly highly expressed in the M1 group. In an analysis of the miRNA target genes, we found that CDH2, KNG1, and MMP2 were correlated with CRC metastasis. We demonstrated a new possible pathway for CRC metastasis: miR-576-5p/F9, miR20a/MMP2, CTSK, MMP3, and miR449a/P2RY14. The regulation of IGF transport and uptake by IGFBPs, extracellular matrix organization, signal transduction and the immune system were the enriched pathways.\nCONCLUSION: This model can predict CRC to liver metastases and the pathways involved, which can be clinically applicable.", "claims": [{"id": "claim-method", "statement": "To identify common differentially expressed genes (DEGs) in the three microarray datasets, we used GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r)[32], an interactive web tool that can compare two or more groups of samples under the same experimental conditions in a GEO dataset, to identify DEGs or differentially expressed miRNAs (DEMs) between primary colorectal tumor and liver metastasis samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30807603", "locator": "sections[4] \"Common genes and miRNAs and the identification of common miRNA targets\" paragraph 2", "quote": "To identify common differentially expressed genes (DEGs) in the three microarray datasets, we used GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r)[32], an interactive web tool that can compare two or more groups of samples under the same experimental conditions in a GEO dataset, to identify DEGs or differentially expressed miRNAs (DEMs) between primary colorectal tumor and liver metastasis samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All relevant data are within the manuscript and its Supporting Information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30807603", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "All relevant data are within the manuscript and its Supporting Information files."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:30807603"], "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. 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"-0.127", "0.012", "0.0005", "-0.739"], ["hsa-miR-488*", "0.099", "0.007", "-0.081", "0.080", "0.009", "-5.021"], ["hsa-miR-637", "0.099", "0.007", "-0.071", "0.096", "0.012", "-0.157"]], "row_count": 34, "column_count": 7, "numeric_cells": 212, "header_rows": 0, "locator": "section[9]/table-wrap[1]#pone.0211968.t001"}}, {"id": "asset:table:pmid:30807603:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2cf7969b15a2da182152054ae911cb82dd89e26b35aade8b04c394a6020df0db", "bytes": 900, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#pone.0211968.t002", "version": null, "note": "The common miRNAs and their common gene targets.", "structure": {"pmcid": "PMC6391078", "section_index": 9, "section_title": "Potential miRNA-mRNA interactors in primary CRC tumors and liver metastases", "row_count": 12, "column_count": 4}, "table": 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"table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:01c701ee5f925957ddf428e811b67f5e31ee2bc0aa0ee784cce2270ae447465b", "bytes": 975, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[3]#pone.0211968.t003", "version": null, "note": "The verification of the upregulated miRNAs and their targets in miRDIP tool.", "structure": {"pmcid": "PMC6391078", "section_index": 9, "section_title": "Potential miRNA-mRNA interactors in primary CRC tumors and liver metastases", "row_count": 5, "column_count": 7}, "table": {"label": "Table 3", "caption": "The verification of the upregulated miRNAs and their targets in miRDIP tool.", "rows": [["miRNA", "Precursor", "Targets", "Score", "Class", "Source No.", "Sources"], ["hsa-miR-20a", "miR-20a-5p", "MMP2", "0.70", "Veryhigh", "15", "BiTargeting, DIANA, ElMMo3, MBStar, MAMI, microrna.org, MirAncesTar, miRDB, MirMAP, miRTar2GO, Mirza-G, MultiMiTar, RepTar, TargetRank, TargetScan"], ["CTSK", "0.55", "Veryhigh", "10", "Cupid, DIANA, ElMMo3, MBStar, microrna.org, MirAncesTar, miRDB, MirMAP, Mirza-G, TargetScan"], ["MMP3", "0.47", "Veryhigh", "13", "CoMeTa, DIANA, ElMMo3, MBStar, microrna.org, MirAncesTar, MirMAP, miRTar2GO, Mirza-G, MultiMiTar, RepTar, RNA22, RNAhybrid"], ["hsa-miR-449a", "miR-449a", "P2RY14", "0.39", "Veryhigh", "12", "BCmicrO, DIANA, ElMMo3, MBStar, microrna.org, MirAncesTar, miRDB, MirMAP, Mirza-G, RepTar, RNAhybrid, TargetRank"]], "row_count": 5, "column_count": 7, "numeric_cells": 14, "header_rows": 1, "locator": "section[9]/table-wrap[3]#pone.0211968.t003"}}, {"id": "asset:table:pmid:30807603:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f425b6a5116052a3222fe1b2bcb2c633df7d4e4aa10d23c17474a11c94558a10", "bytes": 1060, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[4]#pone.0211968.t004", "version": null, "note": "The verification of the downregulated miRNAs and their targets in miRDIP tool.", "structure": {"pmcid": "PMC6391078", "section_index": 9, "section_title": "Potential miRNA-mRNA interactors in primary CRC tumors and liver metastases", "row_count": 6, "column_count": 7}, "table": {"label": "Table 4", "caption": "The verification of the downregulated miRNAs and their targets in miRDIP tool.", "rows": [["miRNA", "Precursor", "Targets", "Score", "Class", "Source No.", "Sources"], ["hsa-miR-495", "miR-495-3p", "CDH2", "0.64", "Veryhigh", "15", "BiTargeting, DIANA, ElMMo3, MBStar, MAMI, microrna.org, MirAncesTar, miRDB, MirMAP, miRTar2GO, Mirza-G, MultiMiTar, RepTar, TargetRank, TargetScan"], ["hsa-miR-382", "miR-382-5p", "FGA", "0.49", "Veryhigh", "12", "BCmicrO, DIANA, ElMMo3, MBStar, microrna.org, MirAncesTar, miRDB, MirMAP, MirTar, Mirza-G, RNAhybrid, TargetRank"], ["hsa-miR-619", 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