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Revealing pathway cross-talk related to diabetes mellitus by Monte Carlo Cross-Validation analysis
- Source :
- Open Life Sciences, Vol 12, Iss 1, Pp 473-480 (2017)
- Publication Year :
- 2017
- Publisher :
- Walter de Gruyter GmbH, 2017.
-
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.
- 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
Subjects
Details
- ISSN :
- 23915412
- Volume :
- 12
- Database :
- OpenAIRE
- Journal :
- Open Life Sciences
- Accession number :
- edsair.doi.dedup.....3a9a252d0e9221bf74d4ae0b2cfeb005