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.