Identification of KIF18B as a Hub Candidate Gene in the Metastasis of Clear Cell Renal Cell Carcinoma by Weighted Gene Co-expression Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32973873", "kind": "science-record", "revision": 4, "content_hash": "sha256:362aa28bb3509b6f3abe569c1ea9ab8c2ca6672739141b6db10bf84337789af8", "created_at": "2026-11-01T15:41:11Z", "updated_at": "2026-11-01T22:02:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of KIF18B as a Hub Candidate Gene in the Metastasis of Clear Cell Renal Cell Carcinoma by Weighted Gene Co-expression Network Analysis.", "doi": "10.3389/fgene.2020.00905", "pmid": "32973873", "authors": ["Huiying Yang", "Yukun Wang", "Ziyi Zhang", "Hua Li"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a common type of fatal malignancy in the urinary system. As the therapeutic strategies of ccRCC are severely limited at present, the prognosis of patients with metastatic carcinoma is usually not promising. Revealing the pathogenesis and identifying hub candidate genes for prognosis prediction and precise treatment are urgently needed in metastatic ccRCC.\nMETHODS: In the present study, we conducted a series of bioinformatics studies with the gene expression profiles of ccRCC samples from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) database for identifying and validating the hub gene of metastatic ccRCC. We constructed a co-expression network, divided genes into co-expression modules, and identified ccRCC-related modules by weighted gene co-expression network analysis (WGCNA) with data from GEO. Then, we investigated the functions of genes in the ccRCC-related modules by enrichment analyses and built a sub-network accordingly. A hub candidate gene of the metastatic ccRCC was identified by maximal clique centrality (MCC) method. We validate the hub gene by differentially expressed gene analysis, overall survival analysis, and correlation analysis with clinical traits with the external dataset (TCGA). Finally, we explored the function of the hub gene by correlation analysis with targets of precise therapies and single-gene gene set enrichment analysis.\nRESULTS: We conducted WGCNA with the expression profiles of GSE73731 from GEO and divided all genes into 8 meaningful co-expression modules. One module is proved to be positively correlated with pathological stage and tumor grade of ccRCC. Genes in the ccRCC-related module were mainly enriched in functions of mitotic cell division and several proverbial tumor related signal pathways. We then identified KIF18B as a hub gene of the metastasis of ccRCC. Validating analyses in external dataset observed the up-regulation of KIF18B in ccRCC and its correlation with worse outcomes. Further analyses found that the expression of KIF18B is related to that of targets of precise therapies.\nCONCLUSION: Our study proposed KIF18B as a hub candidate gene of ccRCC for the first time. Our conclusion may provide a brand-new clue for prognosis evaluating and precise treatment for ccRCC in the future.", "claims": [{"id": "claim-method", "statement": "We conducted WGCNA with the WGCNA package (Langfelder and Horvath, 2008) under R environment.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32973873", "locator": "sections[4] \"Construction of Weighted Co-expression Network and Division of Co-expression Modules\" paragraph 2", "quote": "We conducted WGCNA with the WGCNA package (Langfelder and Horvath, 2008) under R environment."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73731. 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Data obtained from TCGA database is available at: https://portal.gdc.cancer.gov/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:32973873"], "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:GSE73731"], "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:GSE73731"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32973873", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.00905", "sha256": "sha256:df993930fb2a9e079426f2f6e97fdde2469b3945abef1b3b549cdfa2cc62af15", "bytes": 43146, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2020.00905", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7468490", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE73731", "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=GSE73731", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73731", "version": null, "note": "Publicly available datasets were analyzed in this study. 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