ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics

Bioinformatics
Ning ShiShan He

Abstract

Inferring gene regulatory networks from gene expression time series data is important for gaining insights into the complex processes of cell life. A popular approach is to infer Boolean networks. However, it is still a pressing open problem to infer accurate Boolean networks from experimental data that are typically short and noisy. To address the problem, we propose a Boolean network inference algorithm which is able to infer accurate Boolean network topology and dynamics from short and noisy time series data. The main idea is that, for each target gene, we use an And/Or tree ensemble algorithm to select prime implicants of which each is a conjunction of a set of input genes. The selected prime implicants are important features for predicting the states of the target gene. Using these important features we then infer the Boolean function of the target gene. Finally, the Boolean functions of all target genes are combined as a Boolean network. Using the data generated from artificial and real-world gene regulatory networks, we show that our algorithm can infer more accurate Boolean network topology and dynamics from short and noisy time series data than other algorithms. Our algorithm enables us to gain better insights into com...Continue Reading

References

Mar 1, 1969·Journal of Theoretical Biology·S A Kauffman
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·N FriedmanD Pe'er
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hidde de Jong
May 8, 2004·Bioinformatics·Ziv Bar-Joseph
Jul 13, 2004·Journal of Theoretical Biology·Reinhard Laubenbacher, Brandilyn Stigler
Jun 21, 2007·Biostatistics·Holger Schwender, Katja Ickstadt
Sep 18, 2008·Nature Reviews. Molecular Cell Biology·Guy Karlebach, Ron Shamir
Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke
Apr 10, 2010·Bioinformatics·Christoph MüsselHans A Kestler
Oct 12, 2010·PloS One·Vân Anh Huynh-ThuPierre Geurts
Apr 8, 2011·Bioinformatics·Markus MaucherHans A Kestler
Nov 13, 2012·Methods : a Companion to Methods in Enzymology·Assieh Saadatpour, Réka Albert
Mar 19, 2014·Computers in Biology and Medicine·Lian En ChaiZalmiyah Zakaria
Mar 29, 2014·BMC Systems Biology·Paola Vera-LiconaReinhard Laubenbacher
Jun 17, 2014·Bioinformatics·Matthew E StudhamErik L L Sonnhammer
Apr 19, 2016·Scientific Reports·Alexander J Gates, Luis M Rocha
Sep 8, 2016·BMC Bioinformatics·Chee Yee LimBerthold Göttgens

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