Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

Hubert Hackl^1*, Thomas Rainer Burkard^1,3*, Alexander Sturn¹, Renee Rubio², Alexander Schleiffer³, Sun Tian³, John Quackenbush², Frank Eisenhaber³, and Zlatko Trajanoski¹

*These authors contributed equally

Addresses: ¹Institute for Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; ²Dana-Farber Cancer Institute, Department of Biostatistics and Computational Biology, 44 Binney Street, Boston, MA 02115, USA; ³Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, 1030 Vienna, Austria

Correspondence: Zlatko Trajanoski. Email: zlatko.trajanoski@tugraz.at URL:http://genome.tugraz.at

Molecular processes during fat cell development with links to functional annotation and sequence architecture:


• List of relevant adipogenic proteins: [per chapter] [per cluster]
• Additional time points of keysteps: [0h] [6h] [12h] [24h] [48h] [72h] [7d] [14d]
• Metabolic processes and transporters: [0h] [6h] [12h] [24h] [48h] [72h] [7d] [14d] [cluster]
• Cholesterol pathway: [CP]
• Detailed signaling pathways and other processes: [0h] [6h] [12h] [24h] [48h] [72h] [7d] [14d] [cluster]
• Cell cycle processes: [I] [II]

List of additional data files and links:

• Array Design
  • Spot map [txt]
  • EST sequences [zip]
• Expression profiles
  • 780 selected ESTs [xls]
  • 5.205 ESTs selected by ANOVA [xls]
  • Raw data for time point from 7d and 2nd experiment (2 gpr-files from GenePix) [zip]
• Functional annotation
  • Distribution of gene ontology for biological processes during adipocyte differentiation [pdf]
  • List of relevant proteins for annotated ESTs [xls][fasta]
• Validation of expression data
  • Real time RT-PCR [pdf][link]
  • Statistical analysis of independent experiments [xls]
  • Comparison of expression data with distribution of expression in different tissues from gene atlas [png][xls][link]
  • Comparison of expression data to previous studies: Soukas et al. 2001 [png], Ross et al. 2002 [png], Burton et al. 2004 [png]
    Expression levels of ESTs/genes from the current dataset not shared with these datasets [xls]
• Potential regulation by mi-RNAs
• Genes with miRNA motif (seeds 1..8, 2..8, 1..9, 2..9) in 3'UTR [png]
• Significant over representation of miRNA motifs (seed 2..8) in 3'UTR from genes in each cluster [png]
• matches of over represented miRNA motifs in 3'UTR of genes in each cluster (seed 2..8):
       [cl-1] [cl-2] [cl-3] [cl-4] [cl-6] [cl-7] [cl-8] [cl-9] [cl-10] [cl-11] [cl-12]
• Significant over representation of miRNA motifs (seed 2..8) in 3'UTR from genes in each cluster [xls]
• Molecular atlas
• Metabolic pathways [pdf][link]
• Regulation of metabolic pathways by key points (6h,12h,48h,7d) [pdf]
• Cellular localization of gene products involved in metabolism and their gene expression at different time points [pdf]
• Cellular localization of gene products involved in other biological processes and their gene expression at different time points [pdf]
• Signaling networks [pdf][link]
• Extracellular matrix remodelling and cytoskeleton reorganization [pdf][link]
• Cellcycle processes [pdf][link1][link2]
• Cholesterol pathway [pdf][link]
• Promoter analysis
• PPAR (RXR) matrix derived from experimental verified binding sites [pdf]
• TRANSFAC matrices for vertebrates [txt]
• Promoter sequences [fasta]
• Chromosomal mapping
  • Clusterwise mapping of 780 ESTs to all chromosomes [pdf][link]
  • Expression of co-localized ESTs for each chromosome [pdf][link]
  • Statistical analysis of co-localized ESTs for 780 selected ESTs [xls]
  • Statistical analysis of co-localized ESTs for 5.502 ANOVA selected ESTs [xls]

Protocols:

• Microarray cDNA clone growth [pdf]
• Microarray PCR, purification, and storage [pdf]
• Making microarray printing plates [pdf]
• Aminoallyl labeling of RNA for microarrays [pdf]
• Microarray labeled probe hybridization [pdf]
• Image analysis of microarray images [pdf]
• 3T3-L1 adipocyte differentiation [pdf]
• RNA isolation [pdf]
• Real Time RT-PCR with LUX-primers [pdf]