In recent years, the advent of high-throughput analytical techniques, such as microarrays and serial analysis of gene expression (SAGE), has led to a rapid accumulation of biological data. The large size of databases precludes manual analysis and renders unsystematic approaches obsolete. To cope with these new challenges and to facilitate efficient data analyses, numerous academic and commercial software packages and databases have been developed. Yet, genes to which no biological function has been assigned compromise the usability of these data. To facilitate functionally annotating these so-called 'novel genes', an in silico screening of such genes has been developed by focusing especially on their expression patterns, namely their 'tissue-enrichment' and a knowledge database called 'C-It' has been developed. Emphasis has also been placed on 'tissue-specific' isoforms by developing a tool to analyze Affymetrix's Exon Array, called 'Exon Array'.
With these algorithms and tools, ~1,000 genes are currently being annotated, which are enriched in a tissue but have not been characterized. To this end, a project called '1,000 Genes Project' has been initiated to functionally annotate these evolutionary-conserved, tissue-enriched genes with unknown functions using various model organisms (mouse, chicken, and zebrafish) and in vitro models (ES cells). In order to benefit from this project, the author's team are also screening for such genes with possible relations to human diseases by incorporating SNPs information.
In this book, the author considers his team's approach as applied to evolutionary-conserved, heart-enriched genes with unknown functions. All the above mentioned methods have been validated by students working in the field of bioinformatics and developmental biology to provide a step-by-step methodology to obtain highly publishable data as well as knowledge creation that will aid the development of products in which can be used in the field of regenerative medicine.
• A step-by-step procedure is provided, from screening to validations
• For biologists with minimum computation skills, the book provides databases and software (web interface) products to guide them through the screening part
• The focus of this book is not only on screening but also on biological validations in which new knowledge will be created: i.e. annotating (giving functions) to 'novel genes'
- In silico screening - transcriptomics data (UniGene, Microarray, SAGE); proteomics data; binding partners Biological validations - in vitro lentivirus-based siRNA knockdown; morpholino knockdown (chicken cardiomyocytes, zebrafish embryos)
- Example: evolutionary-conserved, heart-enriched genes with unknown function
- Applications to regenerative medicine
The target readers are students and researchers working in the field of all fields of biology, especially developmental biology and bioinformatics. Many of the features and methods will be applicable to those working in R&D to screen for genes and small molecules for regenerative medicine.
Dr. Shizuka Uchida is a group leader at the Max-Planck-Institute for Heart and Lung Research (Bad Nauheim, Germany). He is a trained bioinformatician as well as a developmental biologist focusing especially in the field of adult stem cells. He works in both dry and wet lab to combine the power of computers and data mining methods with state-of-art biological experimental techniques and methods.