Supplementary material for
Molecular processes during fat cell development revealed by gene expression profiling
and functional annotation
Hubert Hackl1*, Thomas Rainer Burkard1,3*, 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 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]