Computational protocol: Prostate cancer-associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4

Similar protocols

Protocol publication

[…] Genomic alterations were identified by querying genomic data from Prostate Adenocarcinoma dataset of TCGA. Comprehensive data of 485 prostate adenocarcinoma cases were retrieved from the TCGA database (http://cancergenome.nih.gov/) regarding RNAseq gene expression (Illumina HiSeq RNASeqV2 Level 3.1.9.0). Annotations regarding SPOP mutation status were obtained from cBioPortal (http://www.cbioportal.org/) on the 06/29/2015 . BRD4 mRNA expression levels were dichotomized into low and high expression categories using a model for classification based on finite normal mixture modeling (mclust 5.1 package, R 3.2.2). Differential gene expression was performed using two-class paired significance of microarray data (SAM 2.0 package, R 3.2.2) and genes considered differentially expressed when FDR < 0.05. […]

Pipeline specifications

Software tools cBioPortal, mclust
Databases TCGA Data Portal
Application RNA-seq analysis
Organisms Homo sapiens