Integrative Transcriptome and Epigenome Analysis of CN-AML

Gene expression was obtained from published microarray data using Affymetrix Human Genome 133 plus 2.0 as well as U133A Gene Chips (accession number: GSE9476, GSE1159, GSE6891, GSE12417) (24 (link),25 (link),27 (link),28 (link)). Seventy-three CN-AML patients with mRNA, microRNA and methylation data were derived from The Cancer Genome Atlas (TCGA) (29 (link)). Design, data quality control and normalization of microarray experiments were in accordance with the standard Affymetrix protocols. Expression of mRNA and microRNA were obtained by high throughout transcriptome sequencing (RNA-seq), while methylation data was obtained by Illumina Infinium 450K BeadChips. The expression level of ANP32A was standardized in normally distributed. Then the appropriate cut-off subdivision value was compared by the 4 quartiles of 185 CN-AML patients, which the median value showed evident distinction (Figure S1A,B,C). Therefore, median value of ANP32A expression was used to classify patients into ANP32A^high and ANP32A^low groups. The expression levels of ERG, DNMT3A, BAALC, WT1 and other genes were obtained using the same strategy.