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Annotating New Genes
From in Silico Screening to Experimental Validation
1st Edition - August 6, 2012
Author: Shizuka Uchida
Hardback ISBN:
9 7 8 - 1 - 9 0 7 5 6 8 - 6 8 - 8
eBook ISBN:
9 7 8 - 1 - 9 0 8 8 1 8 - 1 2 - 6
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… Read more
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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.
- 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
List of figures and tables
Acknowledgements
About the author
Chapter 1: Introduction
Chapter 2: Databases and software to make your research life easier
Abstract:
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?
Abstract:
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
Abstract:
4.1 Introduction
4.2 Concept of in silico screening
4.3 Case study: C-It
Chapter 5: Experimental validation: concepts and practice
Abstract:
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
Abstract:
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
Index
- No. of pages: 196
- Language: English
- Published: August 6, 2012
- Imprint: Woodhead Publishing
- Hardback ISBN: 9781907568688
- eBook ISBN: 9781908818126
SU
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