BioCichlid

BioCichlid

version 2.2.0 (released on Feb 22, 2010)

BioCichlid is a 3D visualization system of time-course microarray data, based on the central dogma. BioCichlid visualizes both physical (protein, signaling) 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 both layers. BioChichlid enhances the interpretation of microarray data and allows us to reveal the underlying mechanisms causing differential gene expressions. BioCichlid is a web-based server and client system, so before starting it, please download the client software here.

Genetic interactions

node size color
edge size color
node label

Gene expression

GPD1,10,10.4899925327898,9.76931390760928,10.4498206324553
GPD2,10,9.52410541805251,8.64965085928717,10.9392649439940
LDHA,10,14.8179900169440,15.9315785844933,16.4258600963628
PKM2,10,9.20017612899685,9.93401428372267,8.9727490482011
AGL,10,13.3696669595621,14.3907351556188,15.7766633009403
GPI,10,12.3356408260009,15.4562840945402,16.1718906139608
TPI1,10,12.7259518516814,15.6239170964120,16.7257977393183
GAPDH,10,10.4724563354294,11.8495611980177,11.4327038226745
GFPT1,10,10.2475475599977,8.59932498272185,8.61139325135746
PGK1,10,16.6779004726009,30.3187885918439,32.8834961831406
PGAM1,10,13.7783695977293,16.1920276443771,16.3194466165197
GPD1,10,10.4899925327898,9.76931390760928,10.4498206324553
PDHX,10,11.1552451684558,9.71324141485894,9.81769540896614
ALDOA,10,12.5355850347846,15.3202685676040,16.0530243338311
GCK,10,8.35754625773436,8.96392385267433,9.66133267905933
SREBF1,10,11.8532778264895,15.5708382259633,16.0642359714121
PFKL,10,11.3658673804285,14.5940852644290,17.0388116098802
PKLR,10,9.81175483608543,10.8737775483418,10.2152512755538
GPD1,10,8.26854852989723,9.3777808420419,8.18860093333225
GPD2,10,11.8777619633833,9.60032041686556,8.91350254214724
LDHA,10,14.1549876972424,15.7895192216816,15.3048142157472
PKM2,10,9.14896236994624,9.49305358635563,10.7729047317250
AGL,10,11.6864118257602,13.5238450579531,10.9891193346601
GPI,10,12.4374946455352,15.5022971651588,20.0802867701401
TPI1,10,11.7776836312015,14.9860025932067,17.4592441213828
GAPDH,10,10.9094617482241,11.6455205432438,12.3811008974888
GFPT1,10,10.3399339110434,9.32182407230487,9.45122546465712
PGK1,10,18.9208122639885,30.342403369508,40.1643906465939
PGAM1,10,14.2754198438525,15.7578360666658,16.1608285651444
GPD1,10,8.26854852989723,9.3777808420419,8.18860093333225
PDHX,10,9.84238158205753,9.64912406573402,8.696364425345
ALDOA,10,13.2533103861750,16.1051237498127,19.0415321979539
GCK,10,8.95112514748137,9.23927238388338,9.17415518096244
SREBF1,10,13.9285272386554,17.1109197725315,16.7857595444431
PFKL,10,12.9224177814339,18.6116325032196,20.4818040713874
PKLR,10,9.0546439637811,10.7598561566283,8.87837600396078

cylinder color
radius scale
duration

Physical interactions

node size color
edge size color
node label

Physical to genetic interactions

edge_size color
signal size color
duration

spatial size settings x_size y_size z_size

Reference: Ishiwata RR, Morioka MS, Ogishima S, Tanaka H. BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. Bioinformatics. 2009 Feb 15;25(4):543-4.

If you have any comments and requests, please contact us: biocichlid@bioinfo.tmd.ac.jp.

Systems Biology Group, Dept. of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University

This work utilizes software developed in whole or in part by the National Laboratory for Applied Network Research (NLANR) at the University of California San Diego's San Diego Supercomputer Center, under a National Science Foundation Cooperative Agreement No. ANI-9807479, and its contributors.