A stationary wavelet entropy-based clustering approach accurately predicts gene expression.
Studying epigenetic landscapes is important to understand the condition for gene regulation. Clustering is a useful approach to study epigenetic landscapes by grouping genes based on their epigenetic conditions. However, classical clustering approaches that often use a representative value of the signals in a fixed-sized window do not fully use the information written in the epigenetic landscapes. Clustering approaches to maximize the information of the epigenetic signals are necessary for better understanding gene regulatory environments. For effective clustering of multidimensional epigenetic signals, we developed a method called Dewer, which uses the entropy of stationary wavelet of epigenetic signals inside enriched regions for gene clustering. Interestingly, the gene expression levels were highly correlated with the entropy levels of epigenetic signals. Dewer separates genes better than a window-based approach in the assessment using gene expression and achieved a correlation coefficient above 0.9 without using any training procedure. Our results show that the changes of the epigenetic signals are useful to study gene regulation.
1 Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania.
Nha
N
Nguyen
An
A
Vo
Inchan
I
Choi
Kyoung-Jae
KJ
Won
D041721:3T3-L1 Cells; D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D019277:Entropy; D044127:Epigenesis, Genetic; D015870:Gene Expression; D051379:Mice; D008957:Models, Genetic; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D058067:Wavelet Analysis
algorithms; gene expression; genetic analysis; genome analysis; next-generation sequencing