The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation

Abstract

Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the “Functional Genomics in Embryonic Stem Cells” consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in “Expression Waves” and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells.

Coordinated waves of gene expression during neuronal differentiation of embryonic stem cells as basis for novel approaches to developmental neurotoxicity testing

“…temporally and spatially shifting activation) of gene expression are known from many pioneering studies of mammalian in vivo CNS development 20 and are, for instance, well characterized in high density and resolution in the hippocampus. 32 Waves have also been defined in vitro in mESCs 17,33 or differentiating embryonic carcinoma cells. 16,34 Here, we extended this concept by relating regulation clusters to underlying biological processes important for toxicity testing.…”

Unique Metabolic Features of Stem Cells, Cardiomyocytes, and Their Progenitors

“…44,72,73 To identify fundamental differentiation networks and pathways during the differentiation of ESCs, we recently published whole-genome gene expression profiling of undifferentiated versus differentiated mESCs. 13,74,75 Unique gene clusters clearly depicting their functional participation both at undifferentiated and specific cell-type-associated lineage specification have been identified using clustering techniques. These gene clusters have been used to capture the enrichment of metabolic biological processes and pathways, particularly those associated with energy substrate metabolism.…”

Ethanol Alters the Balance of Sox2, Oct4, and Nanog Expression in Distinct Subpopulations During Differentiation of Embryonic Stem Cells

“…The temporal gene expression of ES cells during differentiation to various lineages parallels that of in vivo progression [2]. Complex features can be reproduced by mouse and human differentiating ES cells to provide clues for the molecular determinants of processes such as neurogenesis [3,4].…”