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Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation

Robab Hakim-Weber1, Anne-M Krogsdam2, Claus Jørgensen3, Maria Fischer2, Andreas Prokesch4, Juliane G Bogner-Strauss4, Stefan R Bornstein1, Jacob B Hansen5, Lise Madsen67, Karsten Kristiansen6, Zlatko Trajanoski2 and Hubert Hackl2*

Author Affiliations

1 Department of Internal Medicine, Technical University Dresden, Germany

2 Biocenter, Division of Bioinformatics, Innsbruck Medical University, Austria

3 Cell Communication Team, Section of Cell and Molecular Biology, The Institute of Cancer Research, London, UK

4 Institute for Genomics and Bioinformatics, Graz University of Technology, Austria

5 Department of Biomedical Sciences, University of Copenhagen, Denmark

6 Department of Biology, University of Copenhagen, Denmark

7 National Institute of Nutrition and Seafood Research, Bergen, Norway

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BMC Research Notes 2011, 4:157  doi:10.1186/1756-0500-4-157

Published: 26 May 2011

Additional files

Additional file 1:

Gene expression levels (log2-fold change) of 1579 in 6 cluster grouped ESTs at several time points during adipocyte differentiation of MEFs and 3T3-L1 cells (as visualized in Figure 3). ESTs were annotated according to the mouse RefSeq database (NCBI MegaBLAST E-value < 1E-30) and Entrez Gene database. Unique genes within each cluster were identified and overrepresented gene ontology (GO) terms are provided.

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Additional file 2:

Results and primer sequences from q-RT-PCR analysis for validation of microarray experiments and to identify expression levels for specific genes during ME3 and MEFA differentiation.

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Additional file 3:

Statistically overrepresented (p < 0.05) potential transcription factor binding sites (TFBS) identified by in silico analysis of genomic regions from -3 kb to + 2 kb around transcription start sites of genes with increasing gene expression at late stages of adipocyte differentiation (cluster F) using position frequency (weight) matrices from TRANSFAC and JASPAR. Corresponding sequence logos from http://genome.tugraz.at/Logo webcite are shown and number of targets within the dataset (cluster) is given and tested against the number of targets from all RefSeq transcripts using Fishers exact test. Note only transcription factor motifs are considered which are exclusively overrepresented in cluster F.

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Additional file 4:

Gene expression levels (log2-fold change) of 3118 ESTs for samples from 3 different time points (d1, d3, d8) related to d0 immediately before hormonal induction of Rb-/- MEF (ME3) and Rb+/+ MEF (MEFA) differentiation. Several distance measures between the expression profiles of the two cell differentiation models (sum of differences, Manhattan distance, Euclidean distance, Pearson correlation coefficient) are provided. Unique genes upregulated (sum of differences > 4) and downregulated (sum of differences < -4) in the ME3 cell differentiation model compared to the MEFA differentiation are emphasized and overrepresented gene ontology (GO) terms are provided.

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Additional file 5:

Gene set enrichment analysis of the gene list from comparison of Rb-/- MEFs and Rb+/+ MEFs during adipocyte differentiation ranked by sum of differences in a gene set of significantly upregulated (log2-fold change > 2) genes in brown adipose tissue versus white adipose tissue [46]and in a gene set with significantly upregulated (log2-fold change > 1) genes in brown versus white preadipocytes at the differentiating stages [47].

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