Computational Biology of Embryonic Stem Cells

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Computational biology in combination with large-scale biology has played a critical role in exploring the great potentials of embryonic stem cells, resulting in significant discoveries. This e-book ...
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The FunGenES Database: A Reference and Discovery Tool for Embryonic Stem Cells and their Derivatives

Pp. 230-245 (16)

Antonis K. Hatzopoulos

Abstract

The “Functional Genomics in Embryonic Stem Cells” (FunGenES) database is based on gene expression profiling data obtained in selected pluripotent mouse Embryonic Stem (ES) cell lines using Affymetrix Mouse 430 v.2 arrays. The interactive FunGenES database allows users to derive gene expression profiles for every transcript that is included in the microarrays, or perform a series of gene association studies to search for groups of co-expressed and thus possibly co-regulated genes during ES cell growth and differentiation. It also includes advanced annotation tools and numerous connections to external reference tools and databases, linking gene expression patterns in stem cells to vital information about the role of corresponding genes in embryonic development or adult homeostasis and disease. In this chapter, I have used specific gene query examples to highlight the potential of the FunGenES database as a reference and discovery tool to study the biology of stem cells.

Keywords:

Functional genomics, Mouse embryonic stem cells, Microarray analysis, FunGenES Database, Gene expression profiling, Bioinformatics, Gene clustering, Time waves, Expression waves, Pathway animations, Multi-Experiment Matrix, g:Profiler.

Affiliation:

Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt Center for Stem Cell Biology, Vanderbilt University, MRB IV - P425C, 2213 Garland Avenue, Nashville, TN 37232-6300, USA