Journal
BMC BIOINFORMATICS
Volume 19, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s12859-018-2100-y
Keywords
Higher-order partial least squares; Chromatin states; Tensor decomposition; Gene expression levels; Histone modification
Categories
Funding
- Fundamental Research Funds for the Central Universities [3102017OQD098]
Ask authors/readers for more resources
Background: Extensive studies have shown that gene expression levels are strongly affected by chromatin mark combinations via at least two mechanisms, i.e., activation or repression. But their combinatorial patterns are still unclear. To further understand the relationship between histone modifications and gene expression levels, here in this paper, we introduce a purely geometric higher-order representation, tensor (also called multidimensional array), which might borrow more unknown interactions in chromatin states to predicting gene expression levels. Results: The prediction models were learned from regions around upstream 10k base pairs and downstream 10k base pairs of the transcriptional start sites (TSSs) on three species (i.e., Human, Rhesus Macaque, and Chimpanzee) with five histone modifications (i.e., H3K4me1, H3K4me3, H3K27ac, H3K27me3, and Pol II). Experimental results demonstrate that the proposed method is more powerful to predicting gene expression levels than several other popular methods. Specifically, our method enable to get more powerful performance on both commonly used criteria, R and RMSE, as high as 1.7% and 11%, respectively. Conclusions: The overall aim of this work is to show that the higher-order representation is able to include more unknown interaction information between histone modifications across different species.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available