Multiplatform Single-Sample Estimates of Transcriptional Activation

• Activity Number: 499
• Type: Contributed
• Date/Time: Wednesday, August 6, 2014 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): W. Evan Johnson*+ and Stephen Piccolo and Andrea Bild
• Companies: Boston University School of Medicine and Boston University and University of Utah
• Keywords: normalization ; data integration ; microarray ; RNA-seq ; mixture model

Abstract

Data integration is crucial to data-generating consortiums, researchers transitioning to newer profiling technologies, and individuals seeking to aggregate data across experiments. We address this need with our Universal exPression Code (UPC) approach, which corrects for platform-specific background noise using models that account for the genomic base composition and length of target regions; this approach also uses a mixture model to estimate whether a gene is active in a particular profiling sample. The latter produces standardized UPC values on a zero-to-one scale, so that they can be interpreted consistently, irrespective of profiling technology, thus enabling downstream analysis pipelines to be developed in a platform-agnostic manner. Furthermore, UPCs are derived using information from within a given sample only-no ancillary samples are required at processing time. Thus, UPCs are suitable for personalized-medicine workflows where samples must be processed individually rather than in batches. In a variety of analyses and comparisons, UPCs perform comparably to other methods designed specifically for microarrays or RNA sequencing in most settings.