title: 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.
authors.affiliation: Max-Delbrück-Center for Molecular Medicine Berlin-Buch, Berlin, Germany.
authors.forename: Herbert
authors.initials: H
authors.lastname: Schulz
authors.forename: Raivo
authors.initials: R
authors.lastname: Kolde
authors.forename: Priit
authors.initials: P
authors.lastname: Adler
authors.forename: Irène
authors.initials: I
authors.lastname: Aksoy
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Anastassiadis
authors.forename: Michael
authors.initials: M
authors.lastname: Bader
authors.forename: Nathalie
authors.initials: N
authors.lastname: Billon
authors.forename: Hélène
authors.initials: H
authors.lastname: Boeuf
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Bourillot
authors.forename: Frank
authors.initials: F
authors.lastname: Buchholz
authors.forename: Christian
authors.initials: C
authors.lastname: Dani
authors.forename: Michael Xavier
authors.initials: MX
authors.lastname: Doss
authors.forename: Lesley
authors.initials: L
authors.lastname: Forrester
authors.forename: Murielle
authors.initials: M
authors.lastname: Gitton
authors.forename: Domingos
authors.initials: D
authors.lastname: Henrique
authors.forename: Jürgen
authors.initials: J
authors.lastname: Hescheler
authors.forename: Heinz
authors.initials: H
authors.lastname: Himmelbauer
authors.forename: Norbert
authors.initials: N
authors.lastname: Hübner
authors.forename: Efthimia
authors.initials: E
authors.lastname: Karantzali
authors.forename: Androniki
authors.initials: A
authors.lastname: Kretsovali
authors.forename: Sandra
authors.initials: S
authors.lastname: Lubitz
authors.forename: Laurent
authors.initials: L
authors.lastname: Pradier
authors.forename: Meena
authors.initials: M
authors.lastname: Rai
authors.forename: Jüri
authors.initials: J
authors.lastname: Reimand
authors.forename: Alexandra
authors.initials: A
authors.lastname: Rolletschek
authors.forename: Agapios
authors.initials: A
authors.lastname: Sachinidis
authors.forename: Pierre
authors.initials: P
authors.lastname: Savatier
authors.forename: Francis
authors.initials: F
authors.lastname: Stewart
authors.forename: Mike P
authors.initials: MP
authors.lastname: Storm
authors.forename: Marina
authors.initials: M
authors.lastname: Trouillas
authors.forename: Jaak
authors.initials: J
authors.lastname: Vilo
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Welham
authors.forename: Johannes
authors.initials: J
authors.lastname: Winkler
authors.forename: Anna M
authors.initials: AM
authors.lastname: Wobus
authors.forename: Antonis K
authors.initials: AK
authors.lastname: Hatzopoulos
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002460:Cell Line; D016000:Cluster Analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D023281:Genomics; D051379:Mice; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction; D012984:Software; D013234:Stem Cells / Q000166:cytology*