scmd: saccharomyces cerevisiae morphological database

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1 h t t p : / / s c m d . g i . k . u - h t t p : / / s c m d . g i . k . u - t o k y o . a c . j p / t o k y o . a c . j p / SCMD: SCMD: Saccharomyces Cerevisiae Saccharomyces Cerevisiae Morphological Database Morphological Database Taro L. Saito Taro L. Saito 1,2 1,2 , Miwaka Ohtani , Miwaka Ohtani 1,2 1,2 , , Hiroshi Sawai Hiroshi Sawai 2 , Fumi Sano , Fumi Sano 2,4 2,4 , , Ayaka Saka Ayaka Saka 2,4 2,4 , Daisuke Watanabe , Daisuke Watanabe 2,4 2,4 , , Masashi Yukawa Masashi Yukawa 2,4 2,4 , , Yoshikazu Ohya Yoshikazu Ohya 2,4 2,4 and Shinichi Morishita and Shinichi Morishita *,2,3 *,2,3 1. 1. Department of Computer Science, Graduate School of Information Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo Science and Technology, University of Tokyo 2. 2. Institute for Bioinformatics and Research and Institute for Bioinformatics and Research and Development, Japan Science and Technology Corporation Development, Japan Science and Technology Corporation . . Department of Computational Biology, Graduate School Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo of Frontier Sciences, University of Tokyo 4. 4. Department of Integrated Biosciences, Graduate School Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo of Frontier Sciences, University of Tokyo

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SCMD: Saccharomyces Cerevisiae Morphological Database. Taro L. Saito 1,2 , Miwaka Ohtani 1,2 , Hiroshi Sawai 2 , Fumi Sano 2,4 , Ayaka Saka 2,4 , Daisuke Watanabe 2,4 , Masashi Yukawa 2,4 , Yoshikazu Ohya 2,4 and Shinichi Morishita *,2,3. - PowerPoint PPT Presentation

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Page 1: SCMD: Saccharomyces Cerevisiae Morphological Database

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SCMD:SCMD: Saccharomyces Cerevisiae Saccharomyces Cerevisiae Morphological DatabaseMorphological Database

Taro L. SaitoTaro L. Saito1,21,2, Miwaka Ohtani, Miwaka Ohtani1,21,2, , Hiroshi SawaiHiroshi Sawai22, Fumi Sano, Fumi Sano2,42,4, , Ayaka SakaAyaka Saka2,42,4, Daisuke Watanabe, Daisuke Watanabe2,42,4, , Masashi YukawaMasashi Yukawa2,42,4, , Yoshikazu OhyaYoshikazu Ohya2,42,4 and Shinichi Morishita and Shinichi Morishita*,2,3*,2,3

1.1. Department of Computer Science, Graduate School of Information Science and Department of Computer Science, Graduate School of Information Science and Technology, University of TokyoTechnology, University of Tokyo

2.2. Institute for Bioinformatics and Research and Development, Japan Institute for Bioinformatics and Research and Development, Japan Science and Technology CorporationScience and Technology Corporation

33 . . Department of Computational Biology, Graduate School of Frontier Department of Computational Biology, Graduate School of Frontier Sciences, University of TokyoSciences, University of Tokyo

4.4. Department of Integrated Biosciences, Graduate School of Frontier Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of TokyoSciences, University of Tokyo

Page 2: SCMD: Saccharomyces Cerevisiae Morphological Database

SCMD: Saccharomyces Cerevisiae Morphological Database

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What is SCMD What is SCMD ??

• SCMD is a collection of micrographs of SCMD is a collection of micrographs of budding yeast mutants.budding yeast mutants.

• Our image processing program, called Our image processing program, called CalMorph, , clips individual cells from clips individual cells from micrographs, then analyzes the micrographs, then analyzes the characteristics of them.characteristics of them.

• Currently following number of yeast mutants and Currently following number of yeast mutants and their micrographs are analyzed. their micrographs are analyzed. • Mutants analyzed: Mutants analyzed: 4,4954,495• Micrographs Processed: Micrographs Processed: 84,40784,407 (x (x

3) 3) • Cells retrieved:Cells retrieved: 1,643,8351,643,835

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MicrographsMicrographs

• Three type of stains are usedThree type of stains are used to see to see – Cell wall Cell wall

• FITC-ConA FITC-ConA – Nucleus locationNucleus location

• DAPI DAPI – Actin distributionActin distribution

• Rh-ph Rh-ph

• All micrographs can be seen in thAll micrographs can be seen in the viewer provided in SCMDe viewer provided in SCMD

Cell wallCell wall NucleusNucleus ActinActin

image processingimage processing

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FITC-ConAFITC-ConA

DAPIDAPI

Rh-phRh-ph

stainstain

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SCMD: Saccharomyces Cerevisiae Morphological Database

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Cell ParametersCell Parameters

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SCMD: Saccharomyces Cerevisiae Morphological Database

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Categorizing by Bud SizeCategorizing by Bud Size

• View of View of ‘group by bud size’ ‘group by bud size’

no budno bud

smallsmall

mediummedium

largelarge

yor202w yor202w his3his3

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Nucleus Location CategoriesNucleus Location Categories

• We categorized the We categorized the states of nucleus states of nucleus locations into 7 locations into 7 groups.groups.

• State A, A1, B, C are State A, A1, B, C are regular status.regular status.

• State D, E, F seldom State D, E, F seldom occur.occur.

Page 8: SCMD: Saccharomyces Cerevisiae Morphological Database

SCMD: Saccharomyces Cerevisiae Morphological Database

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Categorizing by Nucleus LocationCategorizing by Nucleus Location

• View of View of ‘group by nucleus location’‘group by nucleus location’

AA

A1A1

BB

CC

ybl052c ybl052c sas3sas3

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Actin Localization CategoriesActin Localization Categories

Page 10: SCMD: Saccharomyces Cerevisiae Morphological Database

SCMD: Saccharomyces Cerevisiae Morphological Database

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Categorizing by Actin LocalizationCategorizing by Actin Localization

• View of View of ‘group by actin localization’‘group by actin localization’

AA

BB

isoiso

apiapi

EE

FF

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Morphology Search InterfaceMorphology Search Interface

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Searching Similar Shape MutantsSearching Similar Shape Mutants

input shapeinput shape

query resultquery result