Gsrunbrowser

For the exon array analysis, the robust microarray analysis (RMA) algorithm was used for background correction, intra- and intermicroarray normalization, and expression signal calculation [19 (link)]. Significance analysis of microarray (SAM) [20 (link)] was used to calculate significant differential expression. All bioinformatic analyses were performed with the statistical program R, as previously described [21 (link)].
The expression data from quantitative SYBR Green PCR were not normally distributed, so nonparametric tests were used. Expression levels of TET2 in the different groups were analyzed using the Mann-Whitney test with a two-tailed value of P < 0.05 taken as indicating statistical significance. All tests were performed using SPSS v19.0.
Sequencing data from the Sequence Capture experiments were analyzed using GS Run Browser and GS Reference Mapper software, version 2.0.01 (Roche Diagnostics, Mannheim, Germany). All putative variants were compared with published single-nucleotide polymorphism (SNP) data (dbSNP build 130).
Amplicon deep-sequencing data were generated using GS FLX Sequencer Instrument, version 2.3, and analyzed with GS Amplicon Variant Analyzer, version 2.3 (Roche Diagnostics). The results were further processed and visualized following a previously described pipeline [17 (link)].