Annotating New Genes

Annotating New Genes

From in Silico Screening to Experimental Validation

1st Edition - August 6, 2012

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  • Author: Shizuka Uchida
  • Hardcover ISBN: 9781907568688
  • eBook ISBN: 9781908818126

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In recent years, a number of academic and commercial software packages and databases have been developed for the analysis and screening of biological data; however, the usability of these data is compromised by so-called novel genes to which no biological function is assigned. Annotating new genes outlines an approach to the analysis of evolutionary-conserved, heart-enriched genes with unknown functions, offering a step-by-step description of the procedure from screening to validation. The book begins by offering an introduction to the databases and software available, before moving on to cover programming guidelines, including a specific case study on the use of C-It for in silico screening. The second half of the book offers a step-by-step guide to experimental validation concepts and procedures, as well as an overview of additional potential applications of this approach in the field of stem cells and tissue regeneration, before a concluding chapter summarises the concepts and theories presented.

Key Features

  • Focuses not only on screening but also on biological validations
  • Provides details of databases and software (web interface) products for biologists with minimal computation skills
  • Offers a step-by-step outline of the procedure involved


Academics and researchers in the field of bioinformatics and developmental biology; Geneticists and biologists

Table of Contents

  • List of figures and tables


    About the author

    Chapter 1: Introduction

    Chapter 2: Databases and software to make your research life easier


    2.1 Introduction

    2.2 Primary databases

    2.3 Secondary databases

    2.4 Datasets to keep an eye out for

    2.5 Conclusion

    Chapter 3: How to program like a bioinformatician?


    3.1 Introduction

    3.2 Setting up an environment

    3.3 Writing Perl scripts

    3.4 Conclusion

    Chapter 4: Case study: C-It, knowledge database for screening evolutionarily conserved, tissue-enriched, uncharacterized genes


    4.1 Introduction

    4.2 Concept of in silico screening

    4.3 Case study: C-It

    Chapter 5: Experimental validation: concepts and practice


    5.1 Introduction

    5.2 Proposed experimental strategy

    5.3 Step 1: validation of expression patterns

    5.4 Step 2: phenotypic analysis

    5.5 Step 3: molecular interactions

    5.6 Other experiments

    5.7 Conclusion

    Chapter 6: Further application: adult stem cells and tissue regenerations


    6.1 Introduction

    6.2 Cell types in heart and their lineages

    6.3 Current status of cardiac stem cells

    6.4 Conclusion

    Chapter 7: Conclusion


Product details

  • No. of pages: 196
  • Language: English
  • Copyright: © Woodhead Publishing 2012
  • Published: August 6, 2012
  • Imprint: Woodhead Publishing
  • Hardcover ISBN: 9781907568688
  • eBook ISBN: 9781908818126

About the Author

Shizuka Uchida

Shizuka Uchida is a group leader in the Max-Planck Institute for Heart and Lung Research in Bad Nauheim, Germany. He is a trained bioinformatician and a developmental biologist with a specific focus on adult stem cell research, and has extensive experience in combining the power of computers and data mining methods with state-of-the-art experimental techniques.

Affiliations and Expertise

Max-Planck-Institute, Germany

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