Format

Send to

Choose Destination
PLoS Comput Biol. 2018 Mar 14;14(3):e1006019. doi: 10.1371/journal.pcbi.1006019. eCollection 2018 Mar.

iDREM: Interactive visualization of dynamic regulatory networks.

Author information

1
Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.
2
Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego and Rady Children's Hospital, La Jolla, California, United States of America.
3
Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
4
Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America.

Abstract

The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs.

PMID:
29538379
PMCID:
PMC5868853
DOI:
10.1371/journal.pcbi.1006019
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Public Library of Science Icon for PubMed Central
Loading ...
Support Center