Identification of Six Prognostic Genes in EGFR-Mutant Lung Adenocarcinoma Using Structure Network Algorithms.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34868228", "kind": "science-record", "revision": 4, "content_hash": "sha256:8f3100088d1551573548c5f690885d6b3bcef685a68ef8f80a43b86b41bc6be2", "created_at": "2026-11-01T17:36:34Z", "updated_at": "2026-11-01T22:05:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Six Prognostic Genes in EGFR-Mutant Lung Adenocarcinoma Using Structure Network Algorithms.", "doi": "10.3389/fgene.2021.755245", "pmid": "34868228", "authors": ["Haomin Zhang", "Di Lu", "Qinglun Li", "Fengfeng Lu", "Jundong Zhang", "Zining Wang", "Xuechun Lu", "Jinliang Wang"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "This study aims to determine hub genes related to the incidence and prognosis of EGFR-mutant (MT) lung adenocarcinoma (LUAD) with weighted gene coexpression network analysis (WGCNA). From The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we used 253 EGFR-MT LUAD samples and 38 normal lung tissue samples. At the same time, GSE19188 was additionally included to verify the accuracy of the predicted gene. To discover differentially expressed genes (DEGs), the R package \"limma\" was used. The R packages \"WGCNA\" and \"survival\" were used to perform WGCNA and survival analyses, respectively. The functional analysis was carried out with the R package \"clusterProfiler.\" In total, 1450 EGFR-MT-specific DEGs were found, and 7 tumor-related modules were marked with WGCNA. We found 6 hub genes in DEGs that overlapped with the tumor-related modules, and the overexpression level of B3GNT3 was significantly associated with the worse OS (overall survival) of the EGFR-MT LUAD patients (p < 0.05). Functional analysis of the hub genes showed the metabolism and protein synthesis-related terms added value. In conclusion, we used WGCNA to identify hub genes in the development of EGFR-MT LUAD. The established prognostic factors could be used as clinical biomarkers. To confirm the mechanism of those genes in EGFR-MT LUAD, further molecular research is required.", "claims": [{"id": "claim-method", "statement": "The TCGA-LUAD and GSE31210 gene expression data were built using a “WGCNA” package in the form of genetic co-expression modules in R (Zeng et al., 2016).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34868228", "locator": "sections[4] \"Identification of Tumor-Related Modules With WGCNA\" paragraph 2", "quote": "The TCGA-LUAD and GSE31210 gene expression data were built using a “WGCNA” package in the form of genetic co-expression modules in R (Zeng et al., 2016)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found here: GSE31210 GSE19188 https://portal.gdc.cancer.gov/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34868228", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. These data can be found here: GSE31210 GSE19188 https://portal.gdc.cancer.gov/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "WGCNA identified seven tumor-related modules and six overlapping hub genes, with B3GNT3 overexpression significantly associated with worse overall survival in EGFR-mutant LUAD patients.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "We found 6 hub genes in DEGs that overlapped with the tumor-related modules, and the overexpression level of B3GNT3 was significantly associated with the worse OS (overall survival) of the EGFR-MT LUAD patients (p < 0.05)."}, "evidence": [{"asset": "source:pmid:34868228", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 1450 EGFR-MT–specific DEGs were found, and 7 tumor-related modules were marked with WGCNA."}, {"asset": "source:pmid:34868228", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found 6 hub genes in DEGs that overlapped with the tumor-related modules, and the overexpression level of B3GNT3 was significantly associated with the worse OS (overall survival) of the EGFR-MT LUAD patients (p < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "WGCNA identified seven tumor-related modules and six overlapping hub genes, with B3GNT3 overexpression significantly associated with worse overall survival in EGFR-mutant LUAD patients.", "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:34868228"], "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:GSE19188"], "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:GSE19188"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34868228", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2021.755245", "sha256": "sha256:4d7be83d1a93930b404c906bcfec61dd7e401624d421ad82694e3a4e28d91237", "bytes": 35385, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2021.755245", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8635158", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19188", "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=GSE19188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19188", "version": null, "note": "Publicly available datasets were analyzed in this study. 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