Discover regulatory DNA elements using chromatin signatures and artificial neural network

Bioinformatics. 2010 Jul 1;26(13):1579-86. doi: 10.1093/bioinformatics/btq248. Epub 2010 May 7.


Motivation: Recent large-scale chromatin states mapping efforts have revealed characteristic chromatin modification signatures for various types of functional DNA elements. Given the important influence of chromatin states on gene regulation and the rapid accumulation of genome-wide chromatin modification data, there is a pressing need for computational methods to analyze these data in order to identify functional DNA elements. However, existing computational tools do not exploit data transformation and feature extraction as a means to achieve a more accurate prediction.

Results: We introduce a new computational framework for identifying functional DNA elements using chromatin signatures. The framework consists of a data transformation and a feature extraction step followed by a classification step using time-delay neural network. We implemented our framework in a software tool CSI-ANN (chromatin signature identification by artificial neural network). When applied to predict transcriptional enhancers in the ENCODE region, CSI-ANN achieved a 65.5% sensitivity and 66.3% positive predictive value, a 5.9% and 11.6% improvement, respectively, over the previously best approach.

Availability and implementation: CSI-ANN is implemented in Matlab. The source code is freely available at


Supplementary information: Supplementary Materials are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • CD4-Positive T-Lymphocytes / metabolism
  • Chromatin / chemistry*
  • Gene Expression Regulation
  • HeLa Cells
  • Histone Code*
  • Histones / metabolism
  • Humans
  • Neural Networks, Computer
  • Regulatory Sequences, Nucleic Acid*


  • Chromatin
  • Histones