Combinatorial regulation: characteristics of dynamic correlations

IET Systems Biology
J ZhangT Zhou

Abstract

A cis-regulatory module often processes multiple regulatory inputs provided by transcription factors that bind to DNA and regulate the expression of the gene in a combinatorial logic manner. Here the authors analyse dynamic cross correlations between the regulator concentrations and the output of the gene using stochastic modelling, and show their characteristics for different logic operations. The authors find that the dynamic cross-correlation curve with respect to the correlation time near the peak close to the point of the zero correlation time is upwards convex in the case of AND logic whereas downwards convex in the case of OR logic, where intrinsic and extrinsic noise plays a distinct role. This result implies that the cross-correlation function is a useful and robust index for distinguishing super- and sub-additive gene regulatory scenarios (molecular analogues of AND and OR logic operations) that faithfully represent gene expression.

References

Feb 5, 2000·Nature·M B Elowitz, S Leibler
Aug 10, 2000·Cell·T R HughesS H Friend
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
Aug 17, 2002·Science·Michael B ElowitzPeter S Swain
Dec 25, 2002·Bioinformatics·Chad Creighton, Samir Hanash
Apr 11, 2003·Nature·William J BlakeJ J Collins
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Nicolas E BuchlerTerence Hwa
Jun 14, 2003·Proceedings of the National Academy of Sciences of the United States of America·Y SettyU Alon
Jul 11, 2003·Nature·Michael Levine, Robert Tjian
Oct 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·S Mangan, U Alon
Aug 28, 2004·Nature Structural & Molecular Biology·Attila ReményiMatthias Wilmanns
Feb 17, 2005·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Tina L Tootle, Ilaria Rebay
Mar 26, 2005·Science·Juan M Pedraza, Alexander van Oudenaarden
Dec 14, 2005·International Journal of Gynecological Cancer : Official Journal of the International Gynecological Cancer Society·J KaernC Tropé
Mar 8, 2006·Gene Therapy·B Davidson
Mar 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Shota Atsumi, John W Little
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chen-Hsiang Yeang, Tommi Jaakkola
Apr 11, 2006·PLoS Biology·Avraham E MayoUri Alon
Dec 5, 2006·PLoS Computational Biology·Rutger HermsenPieter Rein ten Wolde
Feb 17, 2007·Nature Reviews. Genetics·Gregory A Wray
Feb 24, 2007·Genome Biology·Yoko Shiraishi-Yamaguchi, Teiichi Furuichi
Mar 16, 2007·American Journal of Human Genetics·Christina T L ChenBarak A Cohen
Apr 5, 2007·Nature Protocols·Adam A MargolinAndrea Califano
May 19, 2007·Nature Reviews. Genetics·Uri Alon
Feb 28, 2008·PloS One·Maria I Davidich, Stefan Bornholdt
Jul 23, 2008·Physical Review Letters·Guido NolteKlaus-Robert Müller
Oct 10, 2008·BMC Genomics·Chieh-Chun Chen, Sheng Zhong
Nov 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Aryeh Warmflash, Aaron R Dinner
Nov 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tim Miyashiro, Mark Goulian
Nov 26, 2008·Nature Genetics·Mary J DunlopMichael B Elowitz

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Citations

Aug 8, 2013·IET Systems Biology·Chia-Hua ChuangPo-Kuei Chen

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