Software review
A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks
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* Corresponding author: Shuichi Onami sonami@riken.jp
1 Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, and Advanced Computational Sciences Department, RIKEN Advanced Science Institute, 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan
2 Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama 223-8522, Japan
3 Kitano Symbiotic Systems Project, ERATO, Japan Science and Technology Corporation, M31 6A, 6-31-15 Jingumae, Shibuya, Tokyo 150-0001, Japan
4 The Systems Biology Institute, 5-6-9 Shirokanedai, Minato, Tokyo 108-0071, Japan
5 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
6 Sony Computer Science Laboratories, Inc, 3-14-13 Higashi-gotanda, Shinagawa, Tokyo 141-0022, Japan
Source Code for Biology and Medicine 2011, 6:12 doi:10.1186/1751-0473-6-12
Published: 24 June 2011Abstract
Background
We previously developed the DBRF-MEGN (difference-based regulation finding-minimum equivalent gene network) method, which deduces the most parsimonious signed directed graphs (SDGs) consistent with expression profiles of single-gene deletion mutants. However, until the present study, we have not presented the details of the method's algorithm or a proof of the algorithm.
Results
We describe in detail the algorithm of the DBRF-MEGN method and prove that the algorithm deduces all of the exact solutions of the most parsimonious SDGs consistent with expression profiles of gene deletion mutants.
Conclusions
The DBRF-MEGN method provides all of the exact solutions of the most parsimonious SDGs consistent with expression profiles of gene deletion mutants.