title: CbGRiTS: cerebellar gene regulation in time and space.
abstract: The mammalian CNS is one of the most complex biological systems to understand at the molecular level. The temporal information from time series transcriptome analysis can serve as a potent source of associative information between developmental processes and regulatory genes. Here, we introduce a new transcriptome database called, Cerebellar Gene Regulation in Time and Space (CbGRiTS). This dataset is populated with transcriptome data across embryonic and postnatal development from two standard mouse strains, C57BL/6J and DBA/2J, several recombinant inbred lines and cerebellar mutant strains. Users can evaluate expression profiles across cerebellar development in a deep time series with graphical interfaces for data exploration and link-out to anatomical expression databases. We present three analytical approaches that take advantage of specific aspects of the time series for transcriptome analysis. We demonstrate the use of CbGRiTS dataset as a community resource to explore patterns of gene expression and develop hypotheses concerning gene regulatory networks in brain development.
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Thomas
authors.initials: T
authors.lastname: Ha
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Douglas
authors.initials: D
authors.lastname: Swanson
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Matt
authors.initials: M
authors.lastname: Larouche
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Randy
authors.initials: R
authors.lastname: Glenn
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Dave
authors.initials: D
authors.lastname: Weeden
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Peter
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Hamre
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Langston
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Phillips
authors.affiliation: Department of Computer Science, New Mexico State University, Las Cruces, NM, USA.
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Song
authors.affiliation: Department of Computer Science, New Mexico State University, Las Cruces, NM, USA.
authors.forename: Zhengyu
authors.initials: Z
authors.lastname: Ouyang
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME, USA.
authors.forename: Elissa
authors.initials: E
authors.lastname: Chesler
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME, USA.
authors.forename: Suman
authors.initials: S
authors.lastname: Duvvurru
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME, USA.
authors.forename: Roumyana
authors.initials: R
authors.lastname: Yordanova
authors.affiliation: Department of Molecular Science, University of Tennessee Health Science Center, Memphis, TN, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
authors.forename: Kate
authors.initials: K
authors.lastname: Campbell
authors.affiliation: Department of Biology, Bowdoin College, Brunswick, ME, USA.
authors.forename: Greg
authors.initials: G
authors.lastname: Ricker
authors.affiliation: Department of Biology, Bowdoin College, Brunswick, ME, USA.
authors.forename: Carey
authors.initials: C
authors.lastname: Phillips
authors.affiliation: Bioinformatics Program, Department of Biology, University of Memphis, Memphis, TN, USA.
authors.forename: Ramin
authors.initials: R
authors.lastname: Homayouni
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4. Electronic address: dang@cmmt.ubc.ca.
authors.forename: Dan
authors.initials: D
authors.lastname: Goldowitz
mesh_terms: D000465:Algorithms; D000818:Animals; D002531:Cerebellum / Q000196:embryology* / Q000502:physiology*; D016000:Cluster Analysis; D019295:Computational Biology; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008811:Mice, Inbred DBA; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D013045:Species Specificity; D013997:Time Factors; D059467:Transcriptome
keywords: Cerebellum; Development; Granule cell; Mouse; Transcriptome