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Brain Transcriptome Database (BrainTx, formerly CDT-DB) – Profiling of spatio-temporal gene expression during postnatal development of mouse brain

Yo Shinoda1, Akira Sato1, Tetsushi Sadakata2, Hirozumi Nishibe3, Noriyuki Morita4, Takafumi Inoue5, Michisuke Yuzaki6, Yoko Yamaguchi3 and Teiichi Furuichi1*
  • 1 Tokyo University of Science, Department of Applied Biological Science, Japan
  • 2 Gunma University, Advanced Scientific Research Leaders Development Unit, Japan
  • 3 RIKEN BSI, Japan
  • 4 Yasuda Women's University, Japan
  • 5 Waseda University, Japan
  • 6 Keio University, Japan

The mouse brain develops into functional circuits and architectures during the first few weeks of postnatal life through a series of developmental events that are genetically programmed. To decipher the underlying genetic basis, we have analyzed and systematized the spatiotemporal gene expression profiles during the postnatal mouse brain development, and have created a database named “Brain Transcriptome Database (BrainTx)” The BrainTx is a neuroinformatics database for sharing and mining large amounts of gene expression data in terms of developmental time-series patterns, brain regional and cellular patterns, and tissue distribution patterns obtained by microarray analyses, in situ hybridization analyses, etc. By using the BrainTx, we could in silico identify many genes that are specifically expressed in time and space during brain development. Collectively, our results indicated that the postnatal development of the mouse brain is programmed by thousands of different genes, which exhibit differential expression patterns in time and space in developing mouse brain. Moreover, the BrainTx is a valuable bioinformatics tool for elucidating the molecular basis of brain development. This research was supported by funding from Neuroinformatics Japan Center, RIKEN BSI to INCF Japan Node BrainTx Platform Committee. BrainTx URL: http://www.cdtdb.brain.riken.jp

Acknowledgements

This research was supported by funding from Neuroinformatics Japan Center, RIKEN BSI to INCF Japan Node BrainTx Platform Committee and KAKENHI from Ministry of Education, Culture, Sports, Science and Technology Japan (MEXT).

References

1) Furuichi, T., Shiraishi-Yamaguchi, Y., Sato, A., Sadakata, T., Huang, J., Shinoda, Y., Hayashi, K., Mishima, Y., Tomomura, M., Nishibe, H., and Yoshikawa, F. (2011) Systematizing and cloning of genes involved in the cerebellar cortex circuit development. Neurochem Res. 36:1241-1252. PubMed ID: 21243430

2) Sato, A., Sekine, Y., Saruta, C., Nishibe, H., Morita, N., Sato, Y., Sadakata, T., Shinoda, Y., Kojima, T., and Furuichi, T. (2008) Cerebellar development transcriptome (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum. Neural Networks 21:1056-1069. PubMed ID: 18603407

3) Sato, A., Morita, N., Sadakata, T., Yoshikawa, F., Shiraishi-Yamaguchi, Y., Huang, JH., Shoji, S., Tomomura, M., Sato, Y., Suga, E., Sekine, Y., Kitamura, A., Shibata, Y., Furuichi, T. (2004) Deciphering the genetic blueprint of cerebellar development by the gene expression profiling informatics. Neural Information Processing. Lecture Notes in Computer Science 3316:880-884. Springer-Verlag, Berlin, Heidelberger, Germany. DOI: 10.1007/978-3-540-30499-9_135

4) Kagami, Y., and Furuichi, T. (2001) Investigation of differentially expressed genes during the development of mouse cerebellum. Brain Research Gene Expression Patterns 1:39-59. PubMed ID: 15018818

Keywords: gene transcription, Transcription, Genetic, Databases, Genetic, In Situ Hybridization, Microarray, genechip

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Poster, not to be considered for oral presentation

Topic: Genomics and genetics

Citation: Shinoda Y, Sato A, Sadakata T, Nishibe H, Morita N, Inoue T, Yuzaki M, Yamaguchi Y and Furuichi T (2015). Brain Transcriptome Database (BrainTx, formerly CDT-DB) – Profiling of spatio-temporal gene expression during postnatal development of mouse brain. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00020

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Received: 27 May 2015; Published Online: 05 Aug 2015.

* Correspondence: Prof. Teiichi Furuichi, Tokyo University of Science, Department of Applied Biological Science, Noda, Chiba, 278-8510, Japan, tfuruichi@rs.tus.ac.jp