No abstract

Summary: 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.Availability: MeV version 4.7 is written in Java and is freely available for download under the terms of the open-source Artistic License version 2.0. The website (http://mev.tm4.org/) hosts a full user manual as well as a short quick-start guide suitable for new users.Contact: johnq@jimmy.harvard.edu

No abstract

Despite being extensively characterized structurally and biochemically, the functional role of histone deacetylase 8 (HDAC8) has remained largely obscure due in part to a lack of known cellular substrates. Herein, we describe an unbiased approach using chemical tools in conjunction with sophisticated proteomics methods to identify novel non-histone nuclear substrates of HDAC8, including the tumor suppressor ARID1A. These newly discovered substrates of HDAC8 are involved in diverse biological processes including mitosis, transcription, chromatin remodeling, and RNA splicing and may help guide therapeutic strategies that target the function of HDAC8.