University of Tennessee Mirror
  of the UCSC Genome Browser
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Genome Browser
GeneNetwork
Galaxy
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  About the GeneNetwork
GeneNetwork (GN) is public web service for systems genetics. This service is used to study genetic causes that influence gene expression and that control phenotypes and disease susceptibility. GeneNetwork combines 30 years of open data generated by hundreds of scientists with sequence data (SNPs and indels) and massive transcriptome data sets (array and RNA-seq). GN is an open source project with 10 active mirror and production sites. The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at the University of California Santa Cruz (UCSC). The GeneNetwork/UCSC Genome Browser is a mirror of the main UCSC site that contains custom genomic tracks and a large number of RNA-seq tracks for mouse.
  About the Genome Browser at UTHSC
We are maintaining a custom mirror of the UCSC Genome Browser. Reads from RNA and whole genome sequencing have been aligned to the mouse reference (NCBI37/mm9) and can be visualized as tracks in the Browser. Variants in the DBA/2J genome (relative to C57BL/6J) are displayed as CNVs, Inversions, InDels, and SNPs. RNA-seq data for the whole brain, hippocampus, and eye are provided as separate sections. RNA-seq counts are raw reads adjusted to 50 million aligned tags per sample (across-sample correction) and these can be viewed as individual tracks for each strain or grouped by parental alleles. Tracks are customizable by adjusting the scale, display mode, track height, etc. For technical support, please contact Xusheng Wang (xwang39@uthsc.edu). Support for Galaxy is provided in part by funding from the CITG and NIAAA.
  About the Galaxy at UTHSC
We are currently running a mirror of the Galaxy system developed at Penn State (A. Nekrutenko) and Emory University (J. Taylor) (http://main.g2.bx.psu.edu/). Galaxy is a web-based data analysis and workflow management system designed to handle the massive amounts of data generated by next-generation sequencing (e.g. DNA-seq and RNA-seq) experiments. Galaxy is well-suited for the many types of analysis including: file conversion, alignment to a reference genome, analysis of differential expression, and workflow design. Users can upload their own data as well as access public data generated at UTHSC. Public data sets include genomic sequencing data (DNA-seq) generated for the DBA/2J inbred mouse strain and ribo-minus prepared RNA sequencing data (RNA-seq) for ~40 mouse strains and three tissues. For Galaxy support please contact Lei Yan (lyan6@uthsc.edu). Support for Galaxy is provided in part by funding from the CITG and NIAAA.
  News
April 1, 2011 - Mean expression of the B allele and D allele available
We have uploaded the mean expression of the B allele (C57BL/6J) and D allele (DBA/2J) of 34 BXD strains generated by RNAseq.
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