SCMD - Saccharomyces cerevisiae Morphological Database

NAR Molecular Biology Database Collection entry number 576
Saito T.L.1,3, Nakatani Y.1,3, Sese J.1, Sano F.2,3, Yukawa M.2,3, Ohya Y.2,3 and Morishita S.1,3
1Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashinoha, Kashiwa City, Chiba 277-8562, Japan
2Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
3Institute for Bioinformatics and Research and Development, Japan Science and Technology Corporation, Science Plaza, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan

Database Description

To study the global regulation of cell morphology, a number of groups have recently reported genome-wide screening data for yeast mutants with abnormal morphology. Despite the relatively simple ellipsoidal shape of yeast cells, in the past, cell morphology researchers have processed information on cells manually. These time-consuming, entirely subjective tasks motivated us to develop image-processing software that automatically extracts yeast cells from micrographs and processes them to measure key morphological characteristics such as cell size, roundness, bud neck position angle, nuclear DNA localization and actin localization.

As of August 2004, we have retrieved 1,754,888 cells from 90,696 micrographs of 4,726 mutants using our software, and we have published the results in the Saccharomyces cerevisiae Morphological Database (SCMD), which facilitates the analysis of abnormal cells. Our system provides quantitative data for shapes of the daughter and mother cells, localization of the nuclear DNA and morphology of the actin patches. To search for mutants with similar morphological traits, the system outputs a list of mutants ranked by similarity of average morphological parameters. The SCMD is available at

Recent Developments

As of August 2004, we have almost finished processing the disruptants of 5,000 non-essential genes. Novel, powerful data mining functions are also provided. With regarding the mutants of about 1,000 essential genes, a way of quantifying their morphological parameters has been recently developed by the Ohya's group. These parameters will be collected and will be available from our site in future.


This research has been partly supported by the Institute for Bioinformatics and Research and Development (BIRD) of the Japan Science and Technology Corporation (JST). Special thanks go to ex-members of the SCMD project: Miwaka Ohtani, Hiroshi Sawai, Ayaka Saka and Daisuke Watanabe.

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