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Matlab R2009a License File 277

5. the table presents pcr analysis of scfd1 gene expression in the csf and blood from patients with and without ms as well as in the cerebellum and spinal cord from mice with eae. the pcr analysis was performed on total cdna, which was isolated from the csf or blood of ms patients, the cerebellum or spinal cord of eae mice. the expression was normalized to glyceraldehyde-3-phosphate dehydrogenase (gapdh). the expression in blood and cerebellum was significantly lower in ms patients compared to controls. in contrast, the expression in spinal cord was significantly higher in ms patients compared to controls. no difference in expression was observed between the clinical courses of ms. the table indicates that scfd1 expression in the csf was significantly lower than in the blood, whereas in the spinal cord, the scfd1 expression was higher in eae compared to controls.

6. table 2. heterogeneous expression pattern of each of the 4 groups for differentially expressed genes between control and eae samples. three samples were selected from the control group and each of these three samples were matched with 3 samples from the eae group, hence making it a total of 9 samples. the expression values of genes are calculated by averaging the raw cel files after rma normalizing them. only the genes that were at least two-fold differentially expressed are displayed in the table.

histone acetylation is crucial in a variety of biological processes and diseases. however, the biological consequences and relationship between global histone acetylation and transcription remain elusive. to gain better understanding of the biological impacts of global histone acetylation, we have computationally analyzed the acetylation of histones in the mouse brain using chip-seq data from the encode project. the new method allows the identification of transcription factor binding sites in promoters, introns, 3’untranslated regions (3’utrs), and intergenic regions, as well as polya sites and chromatin states. as a proof-of-principle, we used this method to search for transcription factor binding sites (tfbss) and identified in the brain significant binding sites for hnf-1alpha, ctip2, creb1, and klf4. furthermore, our epigenetic analysis of the mouse brain has provided novel insights of histone acetylation patterns in the regions upstream of genes and the relation of histone acetylation on a global scale with transcription. in addition, our study demonstrates that the combination of efficient chip-seq data processing, chip-seq data analysis, and bioinformatics integration into a computational pipeline provides a more systematic and comprehensive approach to identify and understand the biological impact of histone acetylation.

5. the table presents pcr analysis of scfd1 gene expression in the csf and blood from patients with and without ms as well as in the cerebellum and spinal cord from mice with eae. the pcr analysis was performed on total cdna, which was isolated from the csf or blood of ms patients, the cerebellum or spinal cord of eae mice. the expression was normalized to glyceraldehyde-3-phosphate dehydrogenase (gapdh). the expression in blood and cerebellum was significantly lower in ms patients compared to controls. in contrast, the expression in spinal cord was significantly higher in ms patients compared to controls. no difference in expression was observed between the clinical courses of ms. the table indicates that scfd1 expression in the csf was significantly lower than in the blood, whereas in the spinal cord, the scfd1 expression was higher in eae compared to controls.
6. table 2. heterogeneous expression pattern of each of the 4 groups for differentially expressed genes between control and eae samples. three samples were selected from the control group and each of these three samples were matched with 3 samples from the eae group, hence making it a total of 9 samples. the expression values of genes are calculated by averaging the raw cel files after rma normalizing them. only the genes that were at least two-fold differentially expressed are displayed in the table.
histone acetylation is crucial in a variety of biological processes and diseases. however, the biological consequences and relationship between global histone acetylation and transcription remain elusive. to gain better understanding of the biological impacts of global histone acetylation, we have computationally analyzed the acetylation of histones in the mouse brain using chip-seq data from the encode project. the new method allows the identification of transcription factor binding sites in promoters, introns, 3’untranslated regions (3’utrs), and intergenic regions, as well as polya sites and chromatin states. as a proof-of-principle, we used this method to search for transcription factor binding sites (tfbss) and identified in the brain significant binding sites for hnf-1alpha, ctip2, creb1, and klf4. furthermore, our epigenetic analysis of the mouse brain has provided novel insights of histone acetylation patterns in the regions upstream of genes and the relation of histone acetylation on a global scale with transcription. in addition, our study demonstrates that the combination of efficient chip-seq data processing, chip-seq data analysis, and bioinformatics integration into a computational pipeline provides a more systematic and comprehensive approach to identify and understand the biological impact of histone acetylation.
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