CbGRiTS

Cerebellar gene regulation in time and space

Thomas Ha, Douglas Swanson, Matt Larouche, Randy Glenn, Dave Weeden, Peter Zhang, Kristin Hamre, Michael Langston, Charles Phillips, Mingzhou Song, Zhengyu Ouyang, Elissa Chesler, Suman Duvvurru, Roumyana Yordanova, Yan Cui, Kate Campbell, Greg Ricker, Carey Phillips, Ramin Homayouni, Dan Goldowitz

Research output: Contribution to journalArticle

10 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)18-30
Number of pages13
JournalDevelopmental Biology
Volume397
Issue number1
DOIs
StatePublished - Jan 1 2015

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Genes
Gene Expression Profiling
Transcriptome
Databases
Developmental Genes
Gene Regulatory Networks
Regulator Genes
Inbred C57BL Mouse
Embryonic Development
Gene Expression
Brain
Datasets

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Developmental Biology
  • Cell Biology

Cite this

Ha, T., Swanson, D., Larouche, M., Glenn, R., Weeden, D., Zhang, P., ... Goldowitz, D. (2015). CbGRiTS: Cerebellar gene regulation in time and space. Developmental Biology, 397(1), 18-30. https://doi.org/10.1016/j.ydbio.2014.09.032

CbGRiTS : Cerebellar gene regulation in time and space. / Ha, Thomas; Swanson, Douglas; Larouche, Matt; Glenn, Randy; Weeden, Dave; Zhang, Peter; Hamre, Kristin; Langston, Michael; Phillips, Charles; Song, Mingzhou; Ouyang, Zhengyu; Chesler, Elissa; Duvvurru, Suman; Yordanova, Roumyana; Cui, Yan; Campbell, Kate; Ricker, Greg; Phillips, Carey; Homayouni, Ramin; Goldowitz, Dan.

In: Developmental Biology, Vol. 397, No. 1, 01.01.2015, p. 18-30.

Research output: Contribution to journalArticle

Ha, T, Swanson, D, Larouche, M, Glenn, R, Weeden, D, Zhang, P, Hamre, K, Langston, M, Phillips, C, Song, M, Ouyang, Z, Chesler, E, Duvvurru, S, Yordanova, R, Cui, Y, Campbell, K, Ricker, G, Phillips, C, Homayouni, R & Goldowitz, D 2015, 'CbGRiTS: Cerebellar gene regulation in time and space', Developmental Biology, vol. 397, no. 1, pp. 18-30. https://doi.org/10.1016/j.ydbio.2014.09.032
Ha T, Swanson D, Larouche M, Glenn R, Weeden D, Zhang P et al. CbGRiTS: Cerebellar gene regulation in time and space. Developmental Biology. 2015 Jan 1;397(1):18-30. https://doi.org/10.1016/j.ydbio.2014.09.032
Ha, Thomas ; Swanson, Douglas ; Larouche, Matt ; Glenn, Randy ; Weeden, Dave ; Zhang, Peter ; Hamre, Kristin ; Langston, Michael ; Phillips, Charles ; Song, Mingzhou ; Ouyang, Zhengyu ; Chesler, Elissa ; Duvvurru, Suman ; Yordanova, Roumyana ; Cui, Yan ; Campbell, Kate ; Ricker, Greg ; Phillips, Carey ; Homayouni, Ramin ; Goldowitz, Dan. / CbGRiTS : Cerebellar gene regulation in time and space. In: Developmental Biology. 2015 ; Vol. 397, No. 1. pp. 18-30.
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