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WDDD - Worm Developmental Dynamics Database

NAR Molecular Biology Database Collection entry number 1624
Kyoda, K.1,2,3, Adachi, E. 2,3, Masuda, E. 4, Nagai, Y. 4, Suzuki, Y. 4, Oguro, T. 4, Urai, M. 4, Arai, R. 3, Furukawa, M. 3, Shimada, K. 2, Kuramochi, J. 2, Nagai, E. 2, and Onami, S. 1,2,3,4,5,6
1) Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan

2) Advanced Computational Sciences Department, RIKEN Advanced Science Institute, Yokohama 230-0045, Japan

3) Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan

4) Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Tokyo 102-0081, Japan

5) Graduate School of Science and Technology, Keio University, Yokohama 230-0045, Japan

6) National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-0081, Japan.


Database Description

Worm Developmental Dynamics Database (WDDD) stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference (RNAi). The information was obtained by combining four-dimensional (4D) microscopy and image processing (1,2), and contains the three-dimensional coordinate values of the outlines of nuclear regions and the dynamics of the outlines over time. The database provides free access to 50 sets of quantitative data for wild-type embryos and 136 sets of quantitative data for RNAi embryos corresponding to 72 of the 97 essential embryonic genes on chromosome III. The remaining 15 genes exhibited phenotypes that precluded obtaining the quantitative data, such as sterile phenotype. The database also provides sets of 4D differential interference contrast microscopy images on which the quantitative data was based. The database will provide a novel opportunity for the development of computational methods to obtain fresh insights into the mechanisms of development. The quantitative information and microscopy images can be synchronously viewed through a web browser, which is designed for easy access by experimental biologists. All the information is available online at the WDDD (


This work was supported by KAKENHI (Grant-in-Aid for Scientific Research) on Priority Areas gSystems Genomicsh Grant Number 17017038 and Special Coordination Funds for the Promotion of Science and Technology, from the Ministry of Education, Culture, Sports, Science and Technology of Japan.


1. Hamahashi,S., Onami,S. and Kitano,H. (2005) Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. BMC Bioinformatics, 6, 125.

2. Hamahashi,S., Kitano,H. and Onami,S. (2007) A system for measuring cell division patterns of early Caenorhabditis elegans embryos by using image processing and object tracking. Systems Comput. Jpn., 38, 12-24.

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