1. Revealing pathway cross-talk related to diabetes mellitus by Monte Carlo Cross-Validation analysis
- Author
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Han-Qing Cai, Shi-Hong Lv, and Chun-Jing Shi
- Subjects
0301 basic medicine ,differentially expressed genes ,endocrine system diseases ,General Immunology and Microbiology ,QH301-705.5 ,General Neuroscience ,monte carlo cross-validation ,Computational biology ,Biology ,medicine.disease ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Monte carlo cross validation ,random forest classification ,030104 developmental biology ,Differentially expressed genes ,Diabetes mellitus ,diabetes mellitus ,pathway cross-talk ,medicine ,Biology (General) ,General Agricultural and Biological Sciences - Abstract
ObjectiveTo explore potential functional biomarkers in diabetes mellitus (DM) by utilizing gene pathway cross-talk.MethodsFirstly, potential disrupted pathways that were enriched by differentially expressed genes (DEGs) were identified based on biological pathways downloaded from the Ingenuity Pathways Analysis (IPA) database. In addition, we quantified the pathway crosstalk for each pair of pathways based on Discriminating Score (DS). Random forest (RF) classification was then employed to find the top 10 pairs of pathways with a high area under the curve (AUC) value between DM samples versus normal samples based on 10-fold cross-validation. Finally, a Monte Carlo Cross-Validation was applied to demonstrate the identified pairs of pathways by a mutual information analysis.ResultsA total of 247 DEGs in normal and disease samples were identified. Based on the F-test, 50 disrupted pathways were obtained with false discovery rate (FDR) < 0.01. Simultaneously, after calculating the DS, the top 10 pairs of pathways were selected based on a higher AUC value as measured by RF classification. From the Monte Carlo Cross-Validation, we considered the top 10 pairs of pathways with higher AUC values ranked for all 50 bootstraps as the most frequently detected ones.ConclusionThe pairs of pathways identified in our study might be key regulators in DM.
- Published
- 2017