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


BACKGROUND
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.
Ishiwata
Ryosuke R
RR
Department of Computational Biology, School of Medical Sciences, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan.
Morioka
Masaki S
MS
Ogishima
Soichi
S
Tanaka
Hiroshi
H
D003196:Computer Graphics; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface