Comparative Analysis of AML Gene Expression

RNA-Seq: average gene expression from TCGA AML patients and 5 normal CD34⁺ BM controls was expressed as a mathematical mean and standard error of normalized read counts as provided by DESeq2 [60 (link)]. Significance for differential expression was determined by DESeq2 using the Wald test (default significance test), and adjusted for multiple hypothesis testing using Benjamini-Hochberg FDR [61 ] across all genes tested.
Microarray: Total RNA was harvested from 30 AML patient samples and 8 CD34⁺ bone marrow samples from healthy donors (All Cells) using TRIzoL Reagent (Invitrogen) according to the manufacturer's instructions. Gene expression analysis was carried out using Illumina Human HT-12 V.3 Expression BeadChip (Illumina, San Diego, CA). The beadarray expression data were imported and quantile-normalized using the R statistical computing environment and the beadarray Bioconductor package. Hybridization data and parameter information can be accessed in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo). The GEO platform accession number is GSE65409. The Illumina CHP and CEL file accessions are GSM1595702-GSM1595739. Expression data for ASAH1, ASAH2 and ASAH3 probes were averaged and graphed as relative fluorescence units.