Comparative genome-wide exon expression analyses in glioma cell lines and patient samples. Differential Expression (DE) values are plotted against Alternative Splicing (AS) scores for a defined set of 20,157 RefSeq entries. (A) Plot showing the average of three independent experiments for U251 glioblastoma cells in which FGFR1 exon 3 splicing was changed using targeted antisense morpholino oligonucleotide-treatment. The positions of five RefSeq entries representing FGFR1 are indicated. The inset shows representative RT-PCR results for FGFR1 exon 3 splicing following treatment with the control (MO-C) or antisense (MO-T) oligonucleotide. For data on RefSeq entries with significant values see Additional file 4. (B) Plot showing the genome-wide changes in expression and splicing observed in GBM compared to nontumor brain. For each Ref Seq entry, the values are derived from 24 GBM samples minus 12 nontumor brain samples. Notable RefSeq entries are labeled with their gene names. For data on RefSeq entries with significant values see Additional file 5. The theoretical values for a 5-fold (dashed line) and 10-fold (dotted line) change in exon inclusion are shown. For hybridization intensity maps of the highlighted genes see Additional file 3.