To measure expression of each APL gene copy, we applied qPCR to mRNA samples using specific primer pairs to distinguish between transcripts from each gene.
In the first HMM, to detect copy number, we applied EM algorithm for each chromosome separately, while in the second HMM, we pooled all chromosomes and estimated parameters jointly.
(2) To minimize the effects of paralogs in the identification of single-copy orthologs, we applied a more stringent e -value cutoff of 1 × 10−25 in the BlastP step.
To correct for the possible detection of false paralogous copies, we therefore applied a filter discarding any fragment smaller than 200 bp, and did not take into account families with larger inserts or other problematic features (see Material and Methods).
To analyze possible interaction between WWOX, RUNX2 and VEGFA gene copy number aberrations, we applied Spearman's correlation test.
In order to increase the sensitivity for detecting low copy number changes, we applied a probabilistic approach utilizing t-statistics and the local genomic sequence mapping information of each of the cDNA clones on our arrays.
In addition to leveraging copy number data, we applied GSEA to the gene-expression data used to generate the EZH2 and HDAC4 signatures to identify pathways associated with either EZH2 activation or HDAC4 activation in the signature samples.
In order to obtain independent information on the performance of the different microarray platforms in identifying submicroscopic copy-number variations, we applied a single automated HMM algorithm to the experiments performed in this study (see Table 1).
We applied two different copy number finding algorithms (Birdseye and PennCNV) to data generated by the Affymetrix Genome-Wide Human SNP Array 6.0, an array that was specifically designed to assess copy number states throughout the genome [18].
We applied global DNA copy number and gene-expression profiling in 359 breast tumors.
