title: RNA-Seq analysis in MeV.
abstract: RNA-Seq is an exciting methodology that leverages the power of high-throughput sequencing to measure RNA transcript counts at an unprecedented accuracy. However, the data generated from this process are extremely large and biologist-friendly tools with which to analyze it are sorely lacking. MultiExperiment Viewer (MeV) is a Java-based desktop application that allows advanced analysis of gene expression data through an intuitive graphical user interface. Here, we report a significant enhancement to MeV that allows analysis of RNA-Seq data with these familiar, powerful tools. We also report the addition to MeV of several RNA-Seq-specific functions, addressing the differences in analysis requirements between this data type and traditional gene expression data. These tools include automatic conversion functions from raw count data to processed RPKM or FPKM values and differential expression detection and functional annotation enrichment detection based on published methods.
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors: Eleanor A
authors: EA
authors: Howe
authors: Raktim
authors: R
authors: Sinha
authors: Daniel
authors: D
authors: Schlauch
authors: John
authors: J
authors: Quackenbush
mesh_terms: D003196:Computer Graphics; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D017423:Sequence Analysis, RNA; D012984:Software