4DNvestigator: time series genomic data analysis toolbox

Stephen Lindsly; Can Chen; Sijia Liu; Scott Ronquist; Samuel Dilworth; Michael Perlman; Indika Rajapakse

doi:10.1080/19491034.2021.1910437

4DNvestigator: time series genomic data analysis toolbox

Nucleus. 2021 Dec;12(1):58-64. doi: 10.1080/19491034.2021.1910437.

Authors

Stephen Lindsly¹, Can Chen², Sijia Liu^{3

4}, Scott Ronquist¹, Samuel Dilworth⁵, Michael Perlman⁶, Indika Rajapakse^{1

2}

Affiliations

¹ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
² Department of Mathematics, University of Michigan, Ann Arbor, MI, USA.
³ MIT-IBM Watson AI Lab, IBM Research, Cambridge, MA, USA.
⁴ Department of Computer Science, Michigan State University, MI, USA.
⁵ iReprogram, Ann Arbor, MI, USA.
⁶ Department of Statistics, University of Washington, Seattle, WA, USA.

Abstract

Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the '4DNvestigator', a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.

Keywords: 4DN; centrality; entropy; networks; time series.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Data Analysis*
Genomics*
Time Factors

Grants and funding

This work is supported in part by the Air Force Office of Scientific Research (AFOSR) award FA9550-18-1-0028, the Smale Institute, and the Defense Advanced Research Projects Agency (DARPA) award 140D6319C0020 to iReprogram, LLC.