Research
PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli
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* Corresponding author: Vishwanath R Iyer vishy@mail.utexas.edu
Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA
Genome Biology 2006, 7:R42 doi:10.1186/gb-2006-7-5-r42
Published: 31 May 2006Additional files
Additional File 2:
DAVID analysis of enriched GO categories within Class I, Class II and Class III genes
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Additional File 3:
The graph shows the number of genes with peak expression levels at each of the indicated times after stimulation of quiescent cells, for each of the four treatments. We calculated the peak time for each Class I gene (genes induced by all treatments) for each time course. Data for skin and lung fibroblasts were considered in combination. Since we had two cell lines and three biological repeats of each time course, for each GF treatment, we took the median time point at which a gene showed its peak expression level. We then calculated the percentage of genes peaking at each time point for each treatment. EGF, FGF and PDGF tend to induce their peak expression levels between 2 and 4 hours, but expression peaks in response to serum are delayed up to 8 hours.
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Additional File 4:
Skin fibroblasts were treated with the indicated concentrations of FGF for 2 hours. Higher concentrations resulted in higher expression levels of induced genes, comparable to the expression levels seen after treatment of the same cells with serum. Data have been normalized to the time zero sample value. However, although serum treatment resulted in overall higher expression levels, their peaks of expression were generally delayed as compared to FGF treatment
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Additional File 6:
Relative gene expression levels of quiescent skin fibroblasts and lung fibroblasts are shown such that red indicates high expression in skin fibroblasts and green indicates high expression in lung fibroblasts. The right hand portion of the cluster shows data from this study. Since a common universal reference sample was used in all experiments, we divided the ratio of skin versus reference by the ratio of lung versus reference to obtain skin versus lung data sets from a number of independent replicate experiments. The left hand side shows comparative data from an earlier study [6]
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Additional File 9:
Sequences of all miRNAs included on the miRNA microarray
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