An integrative method to decode regulatory logics in gene transcription

Bin Yan, Daogang Guan, Chao Wang, Junwen Wang, Bing He, Jing Qin, Kenneth R. Boheler, Aiping Lu, Ge Zhang, Hailong Zhu

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Modeling of transcriptional regulatory networks (TRNs) has been increasingly used to dissect the nature of gene regulation. Inference of regulatory relationships among transcription factors (TFs) and genes, especially among multiple TFs, is still challenging. In this study, we introduced an integrative method, LogicTRN, to decode TF-TF interactions that form TF logics in regulating target genes. By combining cis-regulatory logics and transcriptional kinetics into one single model framework, LogicTRN can naturally integrate dynamic gene expression data and TF-DNA-binding signals in order to identify the TF logics and to reconstruct the underlying TRNs. We evaluated the newly developed methodology using simulation, comparison and application studies, and the results not only show their consistence with existing knowledge, but also demonstrate its ability to accurately reconstruct TRNs in biological complex systems.

Original languageEnglish (US)
Article number1044
JournalNature Communications
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2017

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Transcription
genes
logic
Transcription Factors
Genes
Gene Regulatory Networks
gene expression
Gene expression
complex systems
inference
Large scale systems
deoxyribonucleic acid
methodology
Gene Expression
Kinetics
DNA
kinetics
simulation

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

An integrative method to decode regulatory logics in gene transcription. / Yan, Bin; Guan, Daogang; Wang, Chao; Wang, Junwen; He, Bing; Qin, Jing; Boheler, Kenneth R.; Lu, Aiping; Zhang, Ge; Zhu, Hailong.

In: Nature Communications, Vol. 8, No. 1, 1044, 01.12.2017.

Research output: Contribution to journalArticle

Yan, B, Guan, D, Wang, C, Wang, J, He, B, Qin, J, Boheler, KR, Lu, A, Zhang, G & Zhu, H 2017, 'An integrative method to decode regulatory logics in gene transcription', Nature Communications, vol. 8, no. 1, 1044. https://doi.org/10.1038/s41467-017-01193-0
Yan, Bin ; Guan, Daogang ; Wang, Chao ; Wang, Junwen ; He, Bing ; Qin, Jing ; Boheler, Kenneth R. ; Lu, Aiping ; Zhang, Ge ; Zhu, Hailong. / An integrative method to decode regulatory logics in gene transcription. In: Nature Communications. 2017 ; Vol. 8, No. 1.
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