Journal
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
Volume 15, Issue 5, Pages -Publisher
IMPERIAL COLLEGE PRESS
DOI: 10.1142/S0219720017500214
Keywords
Structural control; weighted minimum driver node set; human cancer signaling network; p53-mediate DNA damage response network
Categories
Funding
- National High-tech R&D Program of China (863 Program) [2012AA02A601, 2012AA02A602, 2012AA020409, 2012AA020404, 2012AA02A604, 2014AA021505, 2015AA020101, 2015AA020108]
- National Science and Technology Major Project [2013ZX03005012]
- Fundamental Research Funds for Central Universities [HIT.NSRIF.201652]
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Structural controllability is the generalization of traditional controllability for dynamical systems. During the last decade, interesting biological discoveries have been inferred by applied structural controllability analysis to biological networks. However, false positive/negative information (i.e. nodes and edges) widely exists in biological networks that documented in public data sources, which can hinder accurate analysis of structural controllability. In this study, we propose WDN finder, a comprehensive analysis package that provides structural controllability with consideration of node connection strength in biological networks. When applied to the human cancer signaling network and p53-mediate DNA damage response network, WDN finder shows high accuracy on essential nodes prediction in these networks. Compared to existing methods, WDN finder can significantly narrow down the set of minimum driver node set (MDS) under the restriction of domain knowledge. When using p53-mediate DNA damage response network as illustration, we find more meaningful MDSs by WDN finder. The source code is implemented in python and publicly available together with relevant data on GitHub: https://github.com/dustincys/WDN finder.
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