Multi-levels 3D chromatin interactions prediction using epigenomic profiles

Ziad Al Bkhetan, Dariusz Plewczynski

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Identification of the higher-order genome organization has become a critical issue for better understanding of how one dimensional genomic information is being translated into biological functions. In this study, we present a supervised approach based on Random Forest classifier to predict genome-wide three-dimensional chromatin interactions in human cell lines using 1D epigenomics profiles. At the first level of our in silico procedure we build a large collection of machine learning predictors, each one targets single topologically associating domain (TAD). The results are collected and genome-wide prediction is performed at the second level of multi-scale statistical learning model. Initial tests show promising results confirming the previously reported studies. Results were compared with Hi-C and ChIA-PET experimental data to evaluate the quality of the predictors. The system achieved 0.9 for the area under ROC curve, and 0.86–0.89 for accuracy, sensitivity and specificity.

Original languageEnglish
Title of host publicationFoundations of Intelligent Systems - 23rd International Symposium, ISMIS 2017, Proceedings
EditorsMarzena Kryszkiewicz, Henryk Rybinski, Zbigniew W. Ras, Dominik Slezak, Andrzej Skowron, Annalisa Appice, Andrzej Skowron
PublisherSpringer Verlag
Pages19-28
Number of pages10
ISBN (Print)9783319604374
DOIs
Publication statusPublished or Issued - 2017
Externally publishedYes
Event23rd International Symposium on Methodologies for Intelligent Systems, ISMIS 2017 - Warsaw, Poland
Duration: 26 Jun 201729 Jun 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10352 LNAI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference23rd International Symposium on Methodologies for Intelligent Systems, ISMIS 2017
Country/TerritoryPoland
CityWarsaw
Period26/06/1729/06/17

Keywords

  • 3D chromatin interactions
  • 3D genome organization
  • CTCF motifs
  • ChIA-PET
  • Chromatin contact domains
  • Chromatin looping
  • Epigenomics
  • Hi-C
  • Physical interactions
  • Random Forest
  • Statistical learning
  • Topologically associated domains

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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