title: Transcriptome networks in the mouse retina: An exon level BXD RI database.
abstract: OBJECTIVE
  Differences in gene expression provide diverse retina phenotypes and may also contribute to susceptibility to injury and disease. The present study defines the transcriptome of the retina in the BXD RI strain set, using the Affymetrix Mouse Gene 2.0 ST array to investigate all exons of traditional protein coding genes, non-coding RNAs, and microRNAs. These data are presented in a highly interactive database on the GeneNetwork website.
  
  
  METHODS
  In the Normal Retina Database, the mRNA levels of the transcriptome from retinas was quantified using the Affymetrix Mouse Gene 2.0 ST array. This database consists of data from male and female mice. The data set includes a total of 52 BXD RI strains, the parental strains (C57BL/6J and DBA/2J), and a reciprocal cross.
  
  
  RESULTS
  In combination with GeneNetwork, the Department of Defense (DoD) Congressionally Directed Medical Research Programs (CDMRP) Normal Retina Database provides a large resource for mapping, graphing, analyzing, and testing complex genetic networks. Protein-coding and non-coding RNAs can be used to map quantitative trait loci (QTLs) that contribute to expression differences among the BXD strains and to establish links between classical ocular phenotypes associated with differences in the genomic sequence. Using this resource, we extracted transcriptome signatures for retinal cells and defined genetic networks associated with the maintenance of the normal retina. Furthermore, we examined differentially expressed exons within a single gene.
  
  
  CONCLUSIONS
  The high level of variation in mRNA levels found among the BXD RI strains makes it possible to identify expression networks that underline differences in retina structure and function. Ultimately, we will use this database to define changes that occur following blast injury to the retina.
authors.affiliation: Department of Ophthalmology and Emory Eye Center, Emory University, Atlanta, GA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: King
authors.affiliation: Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN.
authors.forename: Lu
authors.initials: L
authors.lastname: Lu
authors.affiliation: Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Williams
authors.affiliation: Department of Ophthalmology and Emory Eye Center, Emory University, Atlanta, GA.
authors.forename: Eldon E
authors.initials: EE
authors.lastname: Geisert
mesh_terms: D000818:Animals; D003433:Crosses, Genetic; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D016678:Genome; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008811:Mice, Inbred DBA; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D040641:Quantitative Trait Loci; D012333:RNA, Messenger / Q000235:genetics*; D012160:Retina / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger