Classifying lower grade glioma cases according to whole genome gene expression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27677590", "kind": "science-record", "revision": 8, "content_hash": "sha256:4b8664ae7e798fede733591d1ffb55d5ed4a1b761c18e2f42f69111142e3b3c5", "created_at": "2026-11-01T15:40:20Z", "updated_at": "2026-11-01T21:59:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Classifying lower grade glioma cases according to whole genome gene expression.", "doi": "10.18632/oncotarget.12188", "pmid": "27677590", "authors": ["Baoshi Chen", "Tingyu Liang", "Pei Yang", "Haoyuan Wang", "Yanwei Liu", "Fan Yang", "Gan You"], "journal": "Oncotarget", "year": 2016, "abstract": "OBJECTIVE: To identify a gene-based signature as a novel prognostic model in lower grade gliomas.\nRESULTS: A gene signature developed from HOXA7, SLC2A4RG and MN1 could segregate patients into low and high risk score groups with different overall survival (OS), and was validated in TCGA RNA-seq and GSE16011 mRNA array datasets. Receiver operating characteristic (ROC) was performed to show that the three-gene signature was more sensitive and specific than histology, grade, age, IDH1 mutation and 1p/19q co-deletion. Gene Set Enrichment Analysis (GSEA) and GO analysis showed high-risk samples were associated with tumor associated macrophages (TAMs) and highly invasive phenotypes. Moreover, HOXA7-siRNA inhibited migration and invasion in vitro, and downregulated MMP9 at the protein level in U251 glioma cells.\nMETHODS: A cohort of 164 glioma specimens from the Chinese Glioma Genome Atlas (CGGA) array database were assessed as the training group. TCGA RNA-seq and GSE16011 mRNA array datasets were used for validation. Regression analyses and linear risk score assessment were performed for the identification of the three-gene signature comprising HOXA7, SLC2A4RG and MN1.\nCO NCLUSIONS: We established a three-gene signature for lower grade gliomas, which could independently predict overall survival (OS) of lower grade glioma patients with higher sensitivity and specificity compared with other clinical characteristics. These findings indicate that the three-gene signature is a new prognostic model that could provide improved OS prediction and accurate therapies for lower grade glioma patients.", "claims": [{"id": "claim-method", "statement": "OS in high- and low-risk patient groups was estimated by the Kaplan-Meier method and 2-sided log-rank test in GraphPad Prism Version 6.01.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27677590", "locator": "sections[16] \"Statistical analyses\" paragraph 5", "quote": "OS in high- and low-risk patient groups was estimated by the Kaplan-Meier method and 2-sided log-rank test in GraphPad Prism Version 6.01."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A cohort of 164 glioma specimens from the Chinese Glioma Genome Atlas (CGGA) array database were assessed as the training group. Samples were obtained from the Chinese Glioma Genome Atlas (CGGA) dataset (the training set);the TCGA RNA-seq database and GSE16011 array dataset were assessed as independent validation sets. Among the 164 lower grade glioma specimens, 117 grade II and 47 grade III samples were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27677590", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A cohort of 164 glioma specimens from the Chinese Glioma Genome Atlas (CGGA) array database were assessed as the training group."}, {"asset": "source:pmid:27677590", "locator": "sections[12] \"Datasets and patients\" paragraph 2", "quote": "Samples were obtained from the Chinese Glioma Genome Atlas (CGGA) dataset (the training set);the TCGA RNA-seq database and GSE16011 array dataset were assessed as independent validation sets."}, {"asset": "source:pmid:27677590", "locator": "sections[16] \"Statistical analyses\" paragraph 2", "quote": "Among the 164 lower grade glioma specimens, 117 grade II and 47 grade III samples were identified."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We established a three-gene signature for lower grade gliomas, which could independently predict overall survival (OS) of lower grade glioma patients with higher sensitivity and specificity compared with other clinical characteristics.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27677590", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A cohort of 164 glioma specimens from the Chinese Glioma Genome Atlas (CGGA) array database were assessed as the training group. TCGA RNA-seq and GSE16011 mRNA array datasets were used for validation. Regression analyses and linear risk score assessment were performed for the identification of the three-gene signature comprising HOXA7, SLC2A4RG and MN1."}, {"asset": "source:pmid:27677590", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We established a three-gene signature for lower grade gliomas, which could independently predict overall survival (OS) of lower grade glioma patients with higher sensitivity and specificity compared with other clinical characteristics."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We established a three-gene signature for lower grade gliomas, which could independently predict overall survival (OS) of lower grade glioma patients with higher sensitivity and specificity compared with other clinical characteristics.", "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:27677590"], "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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Moreover, HOXA7-siRNA inhibited migration and invasion in vitro, a", "ified in the long OS group. Cell culture and transfection of HOXA7-siRNA Human glioma U251 cells were", "hased from Genepharma (Shanghai, China), and transfected into U251 cells using Lipofectamine™ 2000 (I", "roup. 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SUPPLEMENTARY MATERIALS FIGURE"], "order_basis": "paper_text_order:5904", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["OS in high- and low-risk patient groups was estimated by the Kaplan-Meier method and 2-sided log-rank test in GraphPad Prism Version 6.01."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}