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New Computational Approaches for Analysis of cis-Regulatory Networks

Brown, C. Titus and Rust, Alistair G. and Clarke, Peter J. C. and Pan, Zhengjun and Schilstra, Maria J. and De Buysscher, Tristan and Griffin, Gareth and Wold, Barbara J. and Cameron, R. Andrew and Davidson, Eric H. and Bolouri, Hamid (2002) New Computational Approaches for Analysis of cis-Regulatory Networks. Developmental Biology, 246 (1). pp. 86-102. ISSN 0012-1606. https://resolver.caltech.edu/CaltechAUTHORS:20121024-093005962

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Abstract

The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1006/dbio.2002.0619DOIArticle
http://www.sciencedirect.com/science/article/pii/S0012160602906196PublisherArticle
ORCID:
AuthorORCID
Brown, C. Titus0000-0001-6001-2677
Wold, Barbara J.0000-0003-3235-8130
Cameron, R. Andrew0000-0003-3947-6041
Additional Information:© 2002 Elsevier Science (USA). Received for publication December 21, 2001. Revised February 7, 2002. Accepted February 7, 2002. We thank Drs. Rod Adams, Henry Brzeski, and Jonathan Rast for numerous discussions and helpful feedback. Data for Fig. 3 were generated by Toni Snow and Yinjian Xiong. We also thank the robotics macroarraying facility, supported by NIH Grant RR15044 (to E.H.D.) and by the Caltech Beckman Institute. The software development work reported in this paper was supported in part by UK BBSRC Grant 310/BI012024 to HB, and US NIH Grant GM61005 (to E.H.D. and H.B.). C.T.B. is a participant in the Initiative in Computational Molecular Biology, which is funded by an award from the Burroughs Wellcome Fund Interfaces program.
Funders:
Funding AgencyGrant Number
NIHRR15044
Caltech Beckman InstituteUNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)310/BIO12024
NIHGM61005
Burroughs Wellcome FundUNSPECIFIED
Subject Keywords:sequence annotation; comparative analysis; macroarrays; gene network modeling; computational tools
Issue or Number:1
Record Number:CaltechAUTHORS:20121024-093005962
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20121024-093005962
Official Citation:C.Titus Brown, Alistair G. Rust, Peter J.C. Clarke, Zhengjun Pan, Maria J. Schilstra, Tristan De Buysscher, Gareth Griffin, Barbara J. Wold, R.Andrew Cameron, Eric H. Davidson, Hamid Bolouri, New Computational Approaches for Analysis of cis-Regulatory Networks, Developmental Biology, Volume 246, Issue 1, 1 June 2002, Pages 86-102, ISSN 0012-1606, 10.1006/dbio.2002.0619. (http://www.sciencedirect.com/science/article/pii/S0012160602906196)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:35064
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:24 Oct 2012 16:49
Last Modified:09 Mar 2020 13:19

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