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Annotating New Genes
From in Silico Screening to Experimental Validation
Shizuka Uchida (Author)
9781907568688, Elsevier Science
Hardback, published 6 August 2012
196 pages
23.3 x 15.6 x 1.9 cm, 0.58 kg
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.
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
Subject Areas: Biotechnology [TCB]
