title: Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.
abstract: BACKGROUND
  Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development.
  
  
  RESULTS
  Mouse microarrays with more than 27,000 elements were developed, and transcriptional profiles of 3T3-L1 cells (pre-adipocyte cells) were monitored during differentiation. In total, 780 differentially expressed expressed sequence tags (ESTs) were subjected to in-depth bioinformatics analyses. The analysis of 3'-untranslated region sequences from 395 ESTs showed that 71% of the differentially expressed genes could be regulated by microRNAs. A molecular atlas of fat cell development was then constructed by de novo functional annotation on a sequence segment/domain-wise basis of 659 protein sequences, and subsequent mapping onto known pathways, possible cellular roles, and subcellular localizations. Key enzymes in 27 out of 36 investigated metabolic pathways were regulated at the transcriptional level, typically at the rate-limiting steps in these pathways. Also, coexpressed genes rarely shared consensus transcription-factor binding sites, and were typically not clustered in adjacent chromosomal regions, but were instead widely dispersed throughout the genome.
  
  
  CONCLUSIONS
  Large-scale transcription profiling in conjunction with sophisticated bioinformatics analyses can provide not only a list of novel players in a particular setting but also a global view on biological processes and molecular networks.
authors.affiliation: Institute for Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria. hubert.hackl@tugraz.at
authors.forename: Hubert
authors.initials: H
authors.lastname: Hackl
authors.forename: Thomas Rainer
authors.initials: TR
authors.lastname: Burkard
authors.forename: Alexander
authors.initials: A
authors.lastname: Sturn
authors.forename: Renee
authors.initials: R
authors.lastname: Rubio
authors.forename: Alexander
authors.initials: A
authors.lastname: Schleiffer
authors.forename: Sun
authors.initials: S
authors.lastname: Tian
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Frank
authors.initials: F
authors.lastname: Eisenhaber
authors.forename: Zlatko
authors.initials: Z
authors.lastname: Trajanoski
mesh_terms: D041721:3T3-L1 Cells; D017667:Adipocytes / Q000166:cytology / Q000378:metabolism*; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D002454:Cell Differentiation; D002478:Cells, Cultured; D033481:Chromosomes, Mammalian / Q000235:genetics; D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D005796:Genes / Q000235:genetics; D016678:Genome / Q000235:genetics; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D010641:Phenotype; D011401:Promoter Regions, Genetic / Q000235:genetics; D015203:Reproducibility of Results; D051780:Sterol Regulatory Element Binding Protein 1 / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D051780:Sterol Regulatory Element Binding Protein 1; D014157:Transcription Factors