Journal Article

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

Ryosuke R. Ishiwata, Masaki S. Morioka, Soichi Ogishima and Hiroshi Tanaka

in Bioinformatics

Volume 25, issue 4, pages 543-544
Published in print February 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp008
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network

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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@bioinfo.tmd.ac.jp

Journal Article.  797 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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