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Title: MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis

Abstract

MetNet (http://www.botany.iastate.edu/∼mash/metnetex/metabolicnetex.html) is publicly available software in development for analysis of genome-wide RNA, protein and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyse and model a metabolic and regulatory network map of Arabidopsis , combined with gene expression profiling data. It contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases (TAIR, KEGG, BRENDA) and input from biologists in their area of expertise. FCModeler captures input from MetNetDB in a graphical form. Sub-networks can be identified and interpreted using simple fuzzy cognitive maps. FCModeler is intended to develop and evaluate hypotheses, and provide a modelling framework for assessing the large amounts of data captured by high-throughput gene expression experiments. FCModeler and MetNetDB are currently being extended to three-dimensional virtual reality display. The MetNet map, together with gene expression data, can be viewed using multivariate graphics tools in GGobi linked with the data analytic tools in R. Users can highlight different parts of the metabolic network and see the relevant expression data highlighted in other data plots. Multi-dimensional expression data can be rotated through different dimensions. Statistical analysis can be computedmore » alongside the visual. MetNet is designed to provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term provide the basis for identification of metabolic and regulatory networks that control plant composition and development.« less

Authors:
 [1];  [2];  [3];  [4];  [1];  [1];  [5];  [6];  [6];  [7];  [7];  [7]
  1. Department of Genetics, Cellular and Developmental Biology, Iowa State University, Ames, IA 50011, USA
  2. Department of Genetics, Cellular and Developmental Biology, Iowa State University, Ames, IA 50011, USA, Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
  3. Department of Genetics, Cellular and Developmental Biology, Iowa State University, Ames, IA 50011, USA, Department of Statistics, Iowa State University, Ames, IA 50011, USA
  4. Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
  5. Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA, Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
  6. Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
  7. Department of Statistics, Iowa State University, Ames, IA 50011, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1198268
Grant/Contract Number:  
DEFG0201ER15170
Resource Type:
Published Article
Journal Name:
Comparative and Functional Genomics
Additional Journal Information:
Journal Name: Comparative and Functional Genomics Journal Volume: 4 Journal Issue: 2; Journal ID: ISSN 1531-6912
Publisher:
Hindawi Publishing Corporation
Country of Publication:
Country unknown/Code not available
Language:
English

Citation Formats

Wurtele, Eve Syrkin, Li, Jie, Diao, Lixia, Zhang, Hailong, Foster, Carol M., Fatland, Beth, Dickerson, Julie, Brown, Andrew, Cox, Zach, Cook, Dianne, Lee, Eun-Kyung, and Hofmann, Heike. MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis. Country unknown/Code not available: N. p., 2003. Web. doi:10.1002/cfg.285.
Wurtele, Eve Syrkin, Li, Jie, Diao, Lixia, Zhang, Hailong, Foster, Carol M., Fatland, Beth, Dickerson, Julie, Brown, Andrew, Cox, Zach, Cook, Dianne, Lee, Eun-Kyung, & Hofmann, Heike. MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis. Country unknown/Code not available. doi:10.1002/cfg.285.
Wurtele, Eve Syrkin, Li, Jie, Diao, Lixia, Zhang, Hailong, Foster, Carol M., Fatland, Beth, Dickerson, Julie, Brown, Andrew, Cox, Zach, Cook, Dianne, Lee, Eun-Kyung, and Hofmann, Heike. Wed . "MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis". Country unknown/Code not available. doi:10.1002/cfg.285.
@article{osti_1198268,
title = {MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis},
author = {Wurtele, Eve Syrkin and Li, Jie and Diao, Lixia and Zhang, Hailong and Foster, Carol M. and Fatland, Beth and Dickerson, Julie and Brown, Andrew and Cox, Zach and Cook, Dianne and Lee, Eun-Kyung and Hofmann, Heike},
abstractNote = {MetNet (http://www.botany.iastate.edu/∼mash/metnetex/metabolicnetex.html) is publicly available software in development for analysis of genome-wide RNA, protein and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyse and model a metabolic and regulatory network map of Arabidopsis , combined with gene expression profiling data. It contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases (TAIR, KEGG, BRENDA) and input from biologists in their area of expertise. FCModeler captures input from MetNetDB in a graphical form. Sub-networks can be identified and interpreted using simple fuzzy cognitive maps. FCModeler is intended to develop and evaluate hypotheses, and provide a modelling framework for assessing the large amounts of data captured by high-throughput gene expression experiments. FCModeler and MetNetDB are currently being extended to three-dimensional virtual reality display. The MetNet map, together with gene expression data, can be viewed using multivariate graphics tools in GGobi linked with the data analytic tools in R. Users can highlight different parts of the metabolic network and see the relevant expression data highlighted in other data plots. Multi-dimensional expression data can be rotated through different dimensions. Statistical analysis can be computed alongside the visual. MetNet is designed to provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term provide the basis for identification of metabolic and regulatory networks that control plant composition and development.},
doi = {10.1002/cfg.285},
journal = {Comparative and Functional Genomics},
number = 2,
volume = 4,
place = {Country unknown/Code not available},
year = {2003},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1002/cfg.285

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Cited by: 32 works
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