ArticleCell journal2023
Chronic Obstructive Pulmonary Disease: Novel Genes Detection with Penalized Logistic Regression.
Article in Cell journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed, 3 citations in OpenAlex.
- Genomic Regions Associated with Respiratory Disease in Holstein Calves in the Southern United States.Genes · 2025Article
- Article
- Long-term alterations in lung epithelial cells after EL-RSV infection exacerbate allergic responses through IL-1β-induced pathways.Mucosal immunology · 2024Article
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveThis study aimed to introduce novel techniques for identifying the genes associated with developing chronic obstructive pulmonary disease (COPD) and to prioritize COPD candidate genes using regression methods. MATERIALS AND
methodsThis is a secondary analysis of the data from an experimental study. We used penalized logistic regressions with three different types of penalties included least absolute shrinkage and selection operator (LASSO), minimax concave penalty (MCP), and smoothly clipped absolute deviation (SCAD). The models were trained using genome-wide expression profiling to define gene networks relevant to the COPD stages. A 10-fold cross-validation scheme was used to evaluate the performance of the methods. In addition, we validate our results by the external validity approach. We reported the sensitivity, specificity, and area under curve (AUC) of the models.
resultsThere were 21, 22, and 18 significantly associated genes for LASSO, SCAD, and MCP models, respectively. The most statistically conservative method (detecting less significant features) was MCP detected 18 genes that were all detected by the other two approaches. The most appropriate approach was a SCAD penalized logistic regression (AUC= 96.26, sensitivity= 94.2, specificity= 86.96). In this study, we have a common panel of 18 genes in all three models that show a significant positive and negative correlation with COPD, in which RNF130, STX6, PLCB1, CACNA1G, LARP4B, LOC100507634, SLC38A2, and STIM2 showed the odds ratio (OR) more than 1. However, there was a slight difference between penalized methods.
conclusionRegularization solves the serious dimensionality problem in using this kind of regression. More exploration of how these genes affect the outcome and mechanism is possible more quickly in this manner. The regression-based approaches we present could apply to overcoming this issue.
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