A Systems Biology and LASSO-Based Approach to Decipher the Transcriptome-Interactome Signature for Predicting Non-Small Cell Lung Cancer.

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The present study used gene expression data and interaction networks to develop a highly accurate model with the least absolute shrinkage and selection operator (LASSO) for predicting NSCLC. The differentially expressed genes (DEGs) were identified in NSCLC compared with normal tissues using TCGA and GTEx data. A biological network was constructed using DEGs, and the top 20 upregulated and 20 downregulated hub genes were identified. These hub genes were used to identify signature genes with penalized logistic regression using the LASSO to predict NSCLC. Our model’s development involved the following steps: (i) the dataset was divided into 80% for training (TR) and 20% for testing (TD1); (ii) a LASSO logistic regression analysis was performed on the TR with 10-fold cross-validation and identified a combination of 17 genes as NSCLC predictors, which were used further for development of the LASSO model. The model’s performance was assessed on the TD1 dataset and achieved an accuracy and an area under the curve of the receiver operating characteristics (AUC-ROC) of 0.986 and 0.998, respectively. Furthermore, the performance of the LASSO model was evaluated using three independent NSCLC test datasets (GSE18842, GSE27262, GSE19804) and achieved high accuracy, with an AUC-ROC of >0.99, >0.99, and 0.95, respectively. Based on this study, a web application called NSCLCpred was developed to predict NSCLC.", "claims": [{"id": "claim-method", "statement": "We used the R package glmnet version 4.1-3 to develop a penalized logistic regression LASSO model on the TR dataset with 10-fold cv.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36552262", "locator": "sections[7] \"2.5. Construction of the LASSO Model\" paragraph 2", "quote": "We used the R package glmnet version 4.1-3 to develop a penalized logistic regression LASSO model on the TR dataset with 10-fold cv."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The computer code, LASSO Model, and supporting data of NSCLCpred are available at the GitHub repository (https://github.com/firozimtech/NSCLCpred, accessed on 31 October 2022). The R/Shiny web application of NSCLCpred is available at https://hifzuransari.shinyapps.io/NSCLCpred/ (accessed on 31 October 2022).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36552262", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The computer code, LASSO Model, and supporting data of NSCLCpred are available at the GitHub repository (https://github.com/firozimtech/NSCLCpred, accessed on 31 October 2022). The R/Shiny web application of NSCLCpred is available at https://hifzuransari.shinyapps.io/NSCLCpred/ (accessed on 31 October 2022)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A LASSO logistic regression model using a 17-gene signature predicted NSCLC with an accuracy of 0.986 and an AUC-ROC of 0.998 on TD1.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36552262", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The model’s performance was assessed on the TD1 dataset and achieved an accuracy and an area under the curve of the receiver operating characteristics (AUC-ROC) of 0.986 and 0.998, respectively."}, {"asset": "source:pmid:36552262", "locator": "sections[13] \"3.3. Development of the LASSO Model\" paragraph 2", "quote": "We selected lambda.min (0.0005101641) as the best lambda and identified the 17 important genes with non-zero coefficients (Figure 3C, Table S5)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A LASSO logistic regression model using a 17-gene signature predicted NSCLC with an accuracy of 0.986 and an AUC-ROC of 0.998 on TD1.", "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:36552262"], "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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