Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence

Computational inference of putative functional elements in noncoding DNA sequence can significantly hasten the search for verified functional elements, such as transcription factor binding sites. However, while computational methods are able to identify promising putative elements, the number of regions of interest may remain unrealistic for experimental validation. Visualization of putative functional elements can assist tremendously in identifying the regions of greatest interest; interactive vizualization allows researchers additional means of asking and answering questions about putative elements. For example, interactive visualizations allow one to look at motifs in the context of verified functional elements or other putative elements, interactively altering the amount of information displayed and the level of resolution at which it is displayed. The work presented here describes initial efforts toward interactive visualization of putative functional elements specifically for our work with conserved elements.

[1]  J. Touchman,et al.  Vertebrate genome sequencing: building a backbone for comparative genomics. , 2002, Trends in genetics : TIG.

[2]  Nancy F. Hansen,et al.  Comparative analyses of multi-species sequences from targeted genomic regions , 2003, Nature.

[3]  A. Rzhetsky,et al.  The human ATP-binding cassette (ABC) transporter superfamily. , 2001, Genome research.

[4]  Lawrence. Davis,et al.  Handbook Of Genetic Algorithms , 1990 .

[5]  Carolyn J. Mattingly,et al.  Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference , 2005, 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

[6]  S. Cole,et al.  Toxicological relevance of the multidrug resistance protein 1, MRP1 (ABCC1) and related transporters. , 2001, Toxicology.

[7]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[8]  Marc S Halfon,et al.  Exploring genetic regulatory networks in metazoan development: methods and models. , 2002, Physiological genomics.

[9]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[10]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[11]  W. Miller,et al.  Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. , 2000, Science.

[12]  C. Higgins,et al.  ABC transporters: from microorganisms to man. , 1992, Annual review of cell biology.

[13]  I-Min A. Dubchak,et al.  Active conservation of noncoding sequences revealed by three-way species comparisons. , 2000, Genome research.

[14]  L. Pennacchio,et al.  Comparative genomic tools and databases: providing insights into the human genome. , 2003, The Journal of clinical investigation.

[15]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[16]  Joseph C. Aman,et al.  An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach , 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[17]  G. Fogel,et al.  Discovery of sequence motifs related to coexpression of genes using evolutionary computation. , 2004, Nucleic acids research.

[18]  Dorothea Heiss-Czedik,et al.  An Introduction to Genetic Algorithms. , 1997, Artificial Life.