Inferring gene regulatory networks from time series data using the minimum description length principle

Bioinformatics
Wentao ZhaoEdward R Dougherty

Abstract

A central question in reverse engineering of genetic networks consists in determining the dependencies and regulating relationships among genes. This paper addresses the problem of inferring genetic regulatory networks from time-series gene-expression profiles. By adopting a probabilistic modeling framework compatible with the family of models represented by dynamic Bayesian networks and probabilistic Boolean networks, this paper proposes a network inference algorithm to recover not only the direct gene connectivity but also the regulating orientations. Based on the minimum description length principle, a novel network inference algorithm is proposed that greatly shrinks the search space for graphical solutions and achieves a good trade-off between modeling complexity and data fitting. Simulation results show that the algorithm achieves good performance in the case of synthetic networks. Compared with existing state-of-the-art results in the literature, the proposed algorithm exceptionally excels in efficiency, accuracy, robustness and scalability. Given a time-series dataset for Drosophila melanogaster, the paper proposes a genetic regulatory network involved in Drosophila's muscle development. Available from the authors upon ...Continue Reading

References

Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·N FriedmanD Pe'er
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
Sep 28, 2002·Science·Michelle N ArbeitmanKevin P White
Nov 8, 2003·Science·L GiotJ M Rothberg

Citations

Jun 26, 2007·Nature Methods·Laurence EttwillerJoachim Wittbrodt
Apr 6, 2013·Briefings in Bioinformatics·Dick de RidderMarcel J T Reinders
Apr 3, 2012·Bioinformatics·Robert KüffnerRalf Zimmer
Dec 17, 2009·Journal of Bioinformatics and Computational Biology·Graham J Hickman, T Charlie Hodgman
Jun 28, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Wentao ZhaoEdward R Dougherty
Apr 26, 2008·EURASIP Journal on Bioinformatics & Systems Biology·John DoughertyJaakko Astola
Jul 8, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Wenbin LiuIlya Shmulevich
Apr 22, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Wentao ZhaoEdward R Dougherty
Jan 1, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Anthony Almudevar
Mar 20, 2010·BMC Bioinformatics·Ioannis A MaraziotisDimitris Thanos
Oct 22, 2010·BMC Bioinformatics·Vijender ChaitankarChaoyang Zhang
Mar 6, 2012·BMC Bioinformatics·Jagath C Rajapakse, Piyushkumar A Mundra
Jul 3, 2013·Cell Communication and Signaling : CCS·Panuwat TrairatphisanThomas Sauter
Nov 29, 2012·EURASIP Journal on Bioinformatics & Systems Biology·Bilal WajidHazem Nounou
Jun 11, 2010·BMC Systems Biology·Vijender ChaitankarChaoyang Zhang
Mar 7, 2014·PloS One·Alexandre HayeMarianne Rooman
May 24, 2013·Briefings in Bioinformatics·Yongsoo KimDaehee Hwang
Mar 19, 2014·Computers in Biology and Medicine·Lian En ChaiZalmiyah Zakaria
Jun 12, 2012·Biochimica Et Biophysica Acta·Nguyen Xuan VinhPramod P Wangikar
Dec 25, 2015·Seminars in Cell & Developmental Biology·Zaynab MousavianAli Masoudi-Nejad
Feb 22, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Amina NoorHazem Nounou
Oct 15, 2014·IEEE Transactions on Nanobioscience·Aniruddha MaitiAnirban Mukherjee
May 3, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Wentao ZhaoEdward R Dougherty
Aug 6, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Hongjia OuyangWenbin Liu
Aug 18, 2009·Current Biology : CB·Rachael E JackRoberto Caldara
Jan 14, 2016·IEEE Journal of Biomedical and Health Informatics·Belhassen BayarRoman Shterenberg
Jan 1, 2013·Cells·Alejandro F VillaverdeJulio R Banga
May 3, 2019·BMC Bioinformatics·Arnaud BonnaffouxOlivier Gandrillon
Apr 8, 2017·BioMed Research International·Zhiwei JiXiaoliang Zhu
Jul 3, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Jie FangWenbin Liu
Feb 19, 2019·BioData Mining·Gregory DitzlerHassan M Fathallah-Shaykh
Dec 24, 2018·BMC Systems Biology·Roozbeh DehghannasiriEdward R Dougherty
Apr 18, 2018·Ivan BrugereTanya Y. Berger-Wolf

Related Concepts

In Silico
Drosophila melanogaster
Signal Transduction
Cdna Microarrays
MRNA Differential Display
Drosophila melanogaster Proteins

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.