Boolean network inference from time series data incorporating prior biological knowledge

BMC Genomics
Saad Haider, Ranadip Pal

Abstract

Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In this paper, we analyze the issues involved in estimating a model of a GRN from single cell line time series data with limited time points. We present an inference approach for a Boolean Network (BN) model of a GRN from limited transcriptomic or proteomic time series data based on prior biological knowledge of connectivity, constraints on attractor structure and robust design. We applied our inference approach to 6 time point transcriptomic data on Human Mammary Epithelial Cell line (HMEC) after application of Epidermal Growth Factor (EGF) and generated a BN with a plausible biological structure satisfying the data. We further defined and applied a similarity measure to compare synthetic BNs and BNs generated through the proposed approach constructed from transitions of various paths of the synthetic BNs. We have also compared the performance of our algorithm with two existing BN inference algorithms. Through theoretical analysis and simulations, we showed the rarity of arriving at a BN from limited time series data with p...Continue Reading

References

Dec 24, 2013·Nucleic Acids Research·Dario Ghersi, Mona Singh
Jun 17, 2014·Bioinformatics·Matthew E StudhamErik L L Sonnhammer
May 31, 2015·Bioinformatics·Marta R A MatosLars Kaderali
May 20, 2015·Journal of Theoretical Biology·Bin ShaoQi Ouyang
Apr 23, 2016·Expert Review of Proteomics·Gerhard MayerMichael Kohl
Mar 22, 2018·Frontiers in Genetics·Stalin MuñozDavid A Rosenblueth

Citations

Sep 10, 2005·Bioinformatics·Ranadip PalEdward R Dougherty
Dec 27, 2006·Methods : a Companion to Methods in Enzymology·Jill C Sible, John J Tyson
Dec 17, 2010·Molecular BioSystems·Ritwik K LayekEdward R Dougherty
Apr 6, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Bane VasićAnantha Raman Krishnan

Related Concepts

Epidermal Growth Factor
Mammary Gland
Anatomic Structures
Proteomics
Breast
Epidermal Growth Factor Receptor Binding Activity
Epithelial Cells
Gene Expression Profiles
EGF gene
Epidermal Growth Factor Measurement

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