Open Access Highly Accessed Research article

Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays

Hannah C Cheung12, Keith A Baggerly34, Spiridon Tsavachidis3, Linda L Bachinski5, Valerie L Neubauer5, Tamara J Nixon5, Kenneth D Aldape46, Gilbert J Cote14* and Ralf Krahe245*

Author Affiliations

1 Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA

2 Graduate Program in Genes and Development, University of Texas at Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA

3 Department of Bioinformatics and Computational Biology, University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA

4 Graduate Program in Human and Molecular Genetics, University of Texas at Houston Graduate School of Biomedical Sciences, Houston, TX, 77030, USA

5 Department of Cancer Genetics, University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA

6 Department of Pathology, University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA

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BMC Genomics 2008, 9:216  doi:10.1186/1471-2164-9-216

Published: 12 May 2008

Additional files

Additional file 1:

Published genes reported to have glioma-specific splicing that were plotted in Figure 3A. Gene Information, T-values, p-values for published genes for Figure 3A.

Format: XLS Size: 34KB Download file

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Additional file 2:

In silico genes in Figure 3B. Gene Information, T-values, p-values for in silico genes for Figure 3B.

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Additional file 3:

Hybridization intensity maps for genes identified in Figure 1A and 1B. Gene Information, T-values, p-values for in silico genes for Figure 3B.

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Additional file 4:

RefSeq entries with p-values < 0.05 for Figure 1A. Gene Information, T-values, significant p-values for U251 cells treated with FGFR1 antisense morpholino oligonucleotides for Figure 1A.

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Additional file 5:

RefSeq entries with p-values < 0.05 in the normal brain versus glioma patient samples comparison shown in Figure 1B. Gene Information, T-values, significant p-values for NB vs. GBM data for Figure 1B.

Format: XLS Size: 748KB Download file

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Additional file 6:

Data for RT-PCR validations shown in Figure 2A. Gene Information, T-values, p-values for RT-PCR-tested genes for Figure 2.

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Additional file 7:

Hybridization intensity maps for genes identified in Figure 2. Heat Maps for Figure 2.

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Additional file 8:

Hybridization intensity maps for those genes identified in Figure 3A and 3B. Heat Maps for Figure 3.

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Additional file 9:

Differential expression of RNA processing factors between GBM and nontumor samples. Gene Information, Probeset IDs, Expression-values, and p-values for all genes identified as associated with RNA processing.

Format: XLS Size: 142KB Download file

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Additional file 10:

Top 25 differential probesets with significant differences between the two major clustered groups shown in Figure 4. Gene Information, Probeset IDs, Expression-values, and p-values for genes identified in Figure 4.

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Additional file 11:

Primers used in RT-PCR validations. List of Primers used for RT-PCR reactions.

Format: XLS Size: 28KB Download file

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