How to interpret and integrate multi-omics data at systems level.

Animal Cells and Systems
Gun Tae JungKwoneel Kim

Abstract

Current parallel sequencing technologies generate biological sequence data explosively and enable omics studies that analyze collective biological features. The more omics data that is accumulated, the more they show the regulatory complexity of biological phenotypes. This high order regulatory complexity needs systems-level approaches, including network analysis, to understand it. There are a series of layers in the omics field that are closely connected to each other as described in 'central dogma.' We, therefore, have to not only interpret each single omics layer but also to integrate multi-omics layers systematically to get a full picture of the regulatory landscape of the biological phenotype. Especially, individual omics data has their own adequate biological network to apply systematic analysis appropriately. A full regulatory landscape can only be obtained when multi-omics data are incorporated within adequate networks. In this review, we discuss how to interpret and integrate multi-omics data systematically using recent studies. We also propose an analysis framework for systematic multi-omics interpretation by centering on the transcriptional core regulator, which can be incorporated in all omics networks.

References

Mar 1, 2003·Nature Biotechnology·Matthias Mann, Ole N Jensen
Oct 7, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jessica A HurtJ Keith Joung
Mar 24, 2004·Current Opinion in Chemical Biology·Ole Nørregaard Jensen
Mar 22, 2005·Nature Genetics·Katia BassoAndrea Califano
Jun 16, 2006·BioTechniques·Martin R LarsenOle N Jensen
Aug 22, 2006·Mass Spectrometry Reviews·Katja DettmerBruce D Hammock
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Dec 14, 2007·Nature·Benjamin F CravattJohn R Yates
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Feb 28, 2009·Journal of Cellular Biochemistry·Melissa J Fullwood, Yijun Ruan
Sep 11, 2012·Cell·Shane NephJohn A Stamatoyannopoulos
Jan 26, 2013·Science·Franklin W HuangLevi A Garraway
Oct 31, 2014·Nature Methods·Alexey I Nesvizhskii
Nov 25, 2014·Cell·Thomas RollandMarc Vidal
Jan 26, 2016·Trends in Biotechnology·Katsuyuki YugiShinya Kuroda
Apr 23, 2016·Cell·Yansheng LiuRuedi Aebersold
Oct 28, 2016·Nature Genetics·Kwoneel KimJung Kyoon Choi
Mar 24, 2017·PLoS Computational Biology·Kiwon JangJung Kyoon Choi
May 10, 2017·Nature Genetics·Michael E FeiginDavid A Tuveson
Jun 18, 2017·Cell·Evan A BoyleJonathan K Pritchard
Nov 4, 2017·Current Opinion in Structural Biology·Veronika Csizmok, Julie D Forman-Kay
May 24, 2018·Nature Reviews. Genetics·Ali TorkamaniEric J Topol
Nov 13, 2018·Nucleic Acids Research·Sohyun HwangInsuk Lee
Jan 4, 2019·Nature Communications·Maksim KunitskiReinhard Dörner
Jan 16, 2019·Cancer Cell·Dong-Gi MunDaehee Hwang

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Methods Mentioned

BETA
PCR
immunoprecipitation
Hi-C
two-hybrid
nuclear magnetic resonance

Software Mentioned

ARACNe

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