A novel classification method for NSCLC based on the background interaction network and the edge-perturbation matrix.

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Based on edge perturbation, functional gene interaction networks were used to reveal the pathological environment of patients with non-small cell carcinoma at the individual level, and to identify cancer subtypes with the same or similar status, and then a multi-dimensional and multi-omics comprehensive analysis was put into practice. Two edge perturbation subtypes were identified through the construction of the background interaction network and the edge-perturbation matrix (EPM). Further analyses revealed clear differences between those two clusters in terms of prognostic survival, stemness indices, immune cell infiltration, immune checkpoint molecular expression, copy number alterations, mutation load, homologous recombination defects (HRD), neoantigen load, and chromosomal instability. Additionally, a risk prediction model based on TCGA for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) was successfully constructed and validated using the independent data set (GSE50081).", "claims": [{"id": "claim-method", "statement": "According to the Kruskal-Wallis test, the difference of the edge disturbance matrix between the normal and the cancer sample was calculated, and the top 30,000 different edges would be selected according to the level of significant difference", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35398839", "locator": "sections[5] \"Construction of the background interaction network and edge-perturbation matrix\" paragraph 10", "quote": "According to the Kruskal-Wallis test, the difference of the edge disturbance matrix between the normal and the cancer sample was calculated, and the top 30,000 different edges would be selected according to the level of significant difference"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Lung adenocarcinoma (LUAD) and Lung squamous cell carcinoma (LUSC) expression data of the TCGA database, including clinical characteristics and survival information, were downloaded from the UCSC Xena website (https://xenabrowser.net/datapages/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35398839", "locator": "sections[3] \"Published data sets\" paragraph 2", "quote": "Lung adenocarcinoma (LUAD) and Lung squamous cell carcinoma (LUSC) expression data of the TCGA database, including clinical characteristics and survival information, were downloaded from the UCSC Xena website (https://xenabrowser.net/datapages/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two edge perturbation subtypes were identified through the construction of the background interaction network and the edge-perturbation matrix (EPM).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35398839", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Two edge perturbation subtypes were identified through the construction of the background interaction network and the edge-perturbation matrix (EPM)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Two edge perturbation subtypes were identified through the construction of the background interaction network and the edge-perturbation matrix (EPM).", "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:35398839"], "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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