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Bioinformatics Advance Access originally published online on January 6, 2009
Bioinformatics 2009 25(4):543-544; doi:10.1093/bioinformatics/btp008
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network

Ryosuke R. Ishiwata 1,{dagger}, Masaki S. Morioka 1,{dagger}, Soichi Ogishima 2,* and Hiroshi Tanaka 1,2

1Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan

*To whom correspondence should be addressed.


  Abstract

Summary: BioCichlid is a 3D visualization system of time-course microarray data on molecular networks, aiming at interpretation of gene expression data by transcriptional relationships based on the central dogma with physical and genetic interactions. BioCichlid visualizes both physical (protein) and genetic (regulatory) network layers, and provides animation of time-course gene expression data on the genetic network layer. Transcriptional regulations are represented to bridge the physical network (transcription factors) and genetic network (regulated genes) layers, thus integrating promoter analysis into the pathway mapping. BioCichlid enhances the interpretation of microarray data and allows for revealing the underlying mechanisms causing differential gene expressions.

Availability: BioCichlid is freely available and can be accessed at http://newton.tmd.ac.jp/. Source codes for both biocichlid server and client are also available.

Contact: ogishima{at}bioinfo.tmd.ac.jp

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Joaquin Dopazo

Received on August 14, 2008; revised on December 29, 2008; accepted on January 1, 2009

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