2015 Fiscal Year Research-status Report
| Project/Area Number |
25330351
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| Research Institution | Toho University |
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Principal Investigator |
ホセ ナチェル 東邦大学, 理学部, 准教授 (60452984)
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| Project Period (FY) |
2013-04-01 – 2017-03-31
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| Keywords | 構造的な制御問題 / 制御理論 / 支配集合 / ncRNA-たんぱく質相互作用 / たんぱく質相互作用ネットワーク / 情報解析 / 複雑生物情報ネットワーク |
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| Outline of Annual Research Achievements |
In this research project, we focus on developing new methodologies and tools to analyse and control complex biological networks. The Dominating Det (DS) algorithmic framework and related concepts such as Maximum Matching (MM) are used to determine the minimum number of driver nodes required to control the whole complex system. The Minimum Dominating Set (MDS) is defined as the DS of minimum cadinality.
We have extended our previous results to address the problem of determining the control categories such as critical, redudant and intermittent nodes in complex bipartite networks. The newly developed algorithm was then applied to determining associations between human diseases and non-conding RNAs with critical roles in network control.
Moreover, we have developed a new algorithm that provides exact results and identifies the critical control set of nodes up to 180 times faster than previous algorithms, which is a remarkable improvement for obtaining exact results in an NP-hard problem such as MDS. The developed algorithm allowed us a critical controllability analysis of a large integrated biological system composed of a transcriptome- and proteome-wide protein interaction network for the first time.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
The results derived from our analysis and the developed algorithms have been published in recognized journals with impact factor more than 5 and one work was received a Poster Award at the 生命医薬情報学連合大会2015（IIBMP）held in Kyoto. The controllability analysis of non-coding RNA-protein networks (bipartite network) has allowed us to determining associations between human diseases and ncRNAs engaged in critical network control. Moreover, for protein interaction networks (unipartite network), we developed a new algorithm that not only identified the critical control set of proteins by reducing the computational time up to 180 times but also expanded the computable network size up to 25 times. The developed tools allowed us an integrated transcriptome and proteome-wide protein interaction network for the first time which led to unveil relationships between gene co-expression and critical controllability. We also believe that the identified sets of critical control proteins may be of interest as drug targets.
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| Strategy for Future Research Activity |
The newly developed methologies and fast algorithms to address the network controllability features have been applied to important biological systems such as (1) a combination of ncRNA-protein interactions and diseases associations and (2) an integrated transcriptome and protein interaction network.
In this project, we aim at improving the performance of the algorithms to be able to compute the critical controllability problem not only in faster time but also in larger complex networks. The crucial point is to add network structural-based pre-processing steps so that the Integer Linear programming problem becomes easier to solve.
Moreover, we are still progressing on applying the developed critial controllability techniques to address other biological bipartite and directed networks such as metabolic pathways as well as investigating the problem of drug antagonism in the context of network control. In parallel with efficient algorithmic developments and biological data analyses, we are also working on theoretical analyses that uses statistical methods to derive an approximate combinatorial functional equation for the computation of the MDS.
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| Causes of Carryover |
昨年、私は2つの国際会議において研究成果を発表する予定でしたが、一方の国際会議の費用が予算を超えていました。そこで、私は次の年度に、残りの予算を移動することに決めました。
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| Expenditure Plan for Carryover Budget |
今年、2つの国際会議に出席することを計画しています。すでに一つの国際会議で招待講演を依頼されており、これに参加・発表予定です。さらに少なくとももう一つの国際会議に参加・発表を計画しています。
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Research Products
(5 results)
