Hub gene identification and molecular subtype construction for Helicobacter pylori in gastric cancer via machine learning methods and NMF algorithm.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37768204", "kind": "science-record", "revision": 4, "content_hash": "sha256:d4dff5fe59a5ecb145bfbc9aec05bb5905956b8d118ac1c1fc6ea4aaed5d9f21", "created_at": "2026-11-01T19:02:36Z", "updated_at": "2026-11-01T22:52:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hub gene identification and molecular subtype construction for Helicobacter pylori in gastric cancer via machine learning methods and NMF algorithm.", "doi": "10.18632/aging.205053", "pmid": "37768204", "authors": ["Lianghua Luo", "Ahao Wu", "Xufeng Shu", "Li Liu", "Zongfeng Feng", "Qingwen Zeng", "Zhonghao Wang", "Tengcheng Hu", "Yi Cao", "Yi Tu", "Zhengrong Li"], "journal": "Aging", "year": 2023, "abstract": "Helicobacter pylori (HP) is a gram-negative and spiral-shaped bacterium colonizing the human stomach and has been recognized as the risk factor of gastritis, peptic ulcer disease, and gastric cancer (GC). Moreover, it was recently identified as a class I carcinogen, which affects the occurrence and progression of GC via inducing various oncogenic pathways. Therefore, identifying the HP-related key genes is crucial for understanding the oncogenic mechanisms and improving the outcomes of GC patients. We retrieved the list of HP-related gene sets from the Molecular Signatures Database. Based on the HP-related genes, unsupervised non-negative matrix factorization (NMF) clustering method was conducted to stratify TCGA-STAD, GSE15459, GSE84433 samples into two clusters with distinct clinical outcomes and immune infiltration characterization. Subsequently, two machine learning (ML) strategies, including support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF), were employed to determine twelve hub HP-related genes. Beyond that, receiver operating characteristic and Kaplan-Meier curves further confirmed the diagnostic value and prognostic significance of hub genes. Finally, expression of HP-related hub genes was tested by qRT-PCR array and immunohistochemical images. Additionally, functional pathway enrichment analysis indicated that these hub genes were implicated in the genesis and progression of GC by activating or inhibiting the classical cancer-associated pathways, such as epithelial-mesenchymal transition, cell cycle, apoptosis, RAS/MAPK, etc. In the present study, we constructed a novel HP-related tumor classification in different datasets, and screened out twelve hub genes via performing the ML algorithms, which may contribute to the molecular diagnosis and personalized therapy of GC.", "claims": [{"id": "claim-method", "statement": "Then, two classical ML methods, RF and SVM-RFE, were conducted to determine the HP-related hub genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37768204", "locator": "sections[16] \"ML identifying the HP-related hub genes\" paragraph 2", "quote": "Then, two classical ML methods, RF and SVM-RFE, were conducted to determine the HP-related hub genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories (TCGA, https://portal.gdc.cancer.gov/), (GEO, http://www.ncbi.nlm.nih.gov/geo/). The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37768204", "locator": "sections[11] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories (TCGA, https://portal.gdc.cancer.gov/), (GEO, http://www.ncbi.nlm.nih.gov/geo/). The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In the present study, we constructed a novel HP-related tumor classification in different datasets, and screened out twelve hub genes via performing the ML algorithms, which may contribute to the molecular diagnosis and personalized therapy of GC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37768204", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In the present study, we constructed a novel HP-related tumor classification in different datasets, and screened out twelve hub genes via performing the ML algorithms, which may contribute to the molecular diagnosis and personalized therapy of GC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In the present study, we constructed a novel HP-related tumor classification in different datasets, and screened out twelve hub genes via performing the ML algorithms, which may contribute to the molecular diagnosis and personalized therapy of GC.", "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:37768204"], "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:GSE15459"], "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:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37768204", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205053", "sha256": "sha256:5ef18598de3a6e5daa6efc1c7dd79ca07de63ad95aa445b8bcc8ad13c4b2cd7a", "bytes": 59475, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205053", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10683617", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15459", "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=GSE15459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15459", "version": null, "note": "The datasets presented in this study can be found in online repositories (TCGA, https://portal.gdc.cancer.gov/), (GEO, http://www.ncbi.nlm.nih.gov/geo/). 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