Identification of SLITRK6 as a Novel Biomarker in hepatocellular carcinoma by comprehensive bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34754951", "kind": "science-record", "revision": 4, "content_hash": "sha256:b6827c0cf1fbac9baa4a1ba4ec35d649c401229095a28bace54bae8ee8b88702", "created_at": "2026-11-01T17:36:27Z", "updated_at": "2026-11-01T22:05:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of SLITRK6 as a Novel Biomarker in hepatocellular carcinoma by comprehensive bioinformatic analysis.", "doi": "10.1016/j.bbrep.2021.101157", "pmid": "34754951", "authors": ["Xudong Liu", "Yajie Liu", "Zhe Liu", "Yu Zhang", "Ying Ma", "Jiangshan Bai", "Hongmei Yao", "Yafan Wang", "Xue Zhao", "Rui Li", "Xinqiang Song", "Yuxuan Chen", "Zhiguo Feng", "Lei Wang"], "journal": "Biochemistry and biophysics reports", "year": 2021, "abstract": "Hepatocellular carcinoma (HCC) is the most common primary malignancy of the adult liver and morbidity are increasing in recent years, however, there is still no effective strategy to prevent and diagnose HCC. Therefore, it is urgent to research the effective biomarker to predict clinical outcomes of HCC tumorigenesis. In the current study, differentially expressed genes in HCC and normal tissues were investigated using the Gene Expression Omnibus (GEO) dataset GSE144269 and The Cancer Genome Atlas (TCGA). Gene differential expression analysis and weighted correlation network analysis (WGCNA) methods were used to identify nine and 16 key gene modules from the GEO dataset and TCGA dataset, respectively, in which the green module in the GEO dataset and magenta module in TCGA were significantly correlated with HCC occurrence. Third, the enrichment score of gene function annotation results showed that these two key modules focus on the positive regulation of inflammatory response and cell differentiation, etc. Besides, PPI network analysis, mutation analysis, and survival analysis found that SLITRK6 had high connectivity, and its mutation significantly impacted overall survival. In addition, SLITRK6 was found to be low expressed in tumor cells. To summarize, SLITRK6 mutation was found to significantly affect the occurrence and prognosis of HCC. SLITRK6 was confirmed as a new potential gene target for HCC, which may provide a new theoretical basis for personalized diagnosis and chemotherapy of HCC in the future.", "claims": [{"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. GSE144269 and GSE105130 can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) and the gene expression RNA-Seq of TCGA-LIHC from the UCSC Xena database (https://xena.ucsc.edu/). Data will be made available on request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34754951", "locator": "sections[34] \"Data Availability Statement\" paragraphs 1-3", "quote": "Publicly available datasets were analyzed in this study. GSE144269 and GSE105130 can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) and the gene expression RNA-Seq of TCGA-LIHC from the UCSC Xena database (https://xena.ucsc.edu/). Data will be made available on request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SLITRK6 mutation was found to significantly affect the occurrence and prognosis of HCC.", "kind": "quantitative", "target": {"value": 6.0, "unit": "p-value", "tolerance": null, "source": "The results showed that SLITRK6 (P = 6.202e-3) had a significant effect on the overall survival of HCC."}, "evidence": [{"asset": "source:pmid:34754951", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To summarize, SLITRK6 mutation was found to significantly affect the occurrence and prognosis of HCC."}, {"asset": "source:pmid:34754951", "locator": "sections[16] \"SLITRK6 mutation survival analysis and expression analysis\" paragraph 2", "quote": "The results showed that SLITRK6 (P = 6.202e-3) had a significant effect on the overall survival of HCC."}, {"asset": "source:pmid:34754951", "locator": "sections[16] \"SLITRK6 mutation survival analysis and expression analysis\" paragraph 2", "quote": "ROC analysis of normal and tumor diagnosis prediction of SLITRK6 on TCGA-LIHC and GSE144269 data sets showed that the AUC value of the GSE144269 database was 0.874, and that of the TCGA-LIHC database was 0.941 (Fig. 6D and E)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SLITRK6 mutation was found to significantly affect the occurrence and prognosis of HCC.", "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:34754951"], "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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