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.
Reihe
Sprache
Verlagsort
Verlagsgruppe
Elsevier Science & Technology
Zielgruppe
Maße
Höhe: 234 mm
Breite: 156 mm
Gewicht
ISBN-13
978-1-907568-68-8 (9781907568688)
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Schweitzer Klassifikation
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.
Autor*in
Max-Planck-Institute, Germany
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
