The high-throughput measurement devices for DNA, RNA, and proteins produce large amount of information-rich data from biological dynamic systems. It is a need to reverse engineering these data to reveal parameters/structure and behavior relationships implicit in the data. Ultimately, complex interactions between its components that make up a system can be better understood.
However, issues of reverse engineering in bioinformatics like algorithms use, the number of temporal sample, continuous or discrete type of input data, etc. are discussed but merely in the validity problem. We argue that, since the data available in reality are not so perfect, the result of reverse engineering is impacted by the un-perfect data. If this is true, to know how this impacts the results of the reverse engineering and to what extent is an important issue. We choose the parameter estimation as our task of reverse engineering and develop a novel method to investigate this validity problem. The data we used has a minor deviation from real data in each data point and then we compare the results of reverse engineering with its target parameters. It can be realized that the more error in data will introduce more serious validity problem in reverse engineering.
Three artificial systems are used as test bed to demonstrate our approach. The results of the experiments show, a minor deviation in data may introduce large parameter deviation in the parameter solutions. We conclude that we should not ignore the data error in reverse engineering. To have more knowledge of this phenomenon, we further develop an analytical procedure to analyze the dynamic of the systems to see which characteristic will contribute to this impact. The sensitivity test, propagation analysis and impact factor analysis are applied to the systems. Some qualitative rules that describe the relationship between the results of reverse engineering and the dynamics of the system are summarized.
All the finding of this exploration research needs more study to confirm its results. Along this line of research, the biological meaning and the possible relationship between robustness and the variation in parameters in reverse engineering is worth to study in the future. The better reverse algorithm to avoid this validity problem is another topic for future work.
| Identifer | oai:union.ndltd.org:NSYSU/oai:NSYSU:etd-0815106-024707 |
| Date | 15 August 2006 |
| Creators | Chen, Jian-xun |
| Contributors | Tzou Wen Shyong, Tsa Jer Mini, Lee wei po, Chen Chia Mei, Liang Ting Peng, Jeng bing Chiang |
| Publisher | NSYSU |
| Source Sets | NSYSU Electronic Thesis and Dissertation Archive |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0815106-024707 |
| Rights | not_available, Copyright information available at source archive |
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