Annotating New Genes - 1st Edition - ISBN: 9781907568688, 9781908818126

Annotating New Genes

1st Edition

From in Silico Screening to Experimental Validation

Authors: Shizuka Uchida
eBook ISBN: 9781908818126
Hardcover ISBN: 9781907568688
Imprint: Woodhead Publishing
Published Date: 6th August 2012
Page Count: 196
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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



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


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© Woodhead Publishing 2012
Woodhead Publishing
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About the Authors

Shizuka Uchida Author

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