About BrainTx (formerly CDT-DB)

Contents

 
1. Brain Transcriptome Database (BrainTx) Project
 The Brain Transcriptome Database (BrainTx) is a neuroinformatics database that contains gene expression information related to various stages and states of the brain. BrainTx was developed from the Cerebellar Development Transcriptome Database (CDT-DB), which is focused on the transcriptome related to mouse cerebellar development. (Information about CDT-DB can be downloaded using the "Download" option in the menu bar.) The BrainTx project is supported by the Neuroinformatics Japan Center (NIJC) and the Japan-Node of the International Neuroinformatics Coordinating Facility (INCF).
1-1. About BrainTx
 The brain is a very complex structure and its design, which must be encoded in the genome, is attributable to the controlled expression of thousands of specific genes in time and space. The initial aim of the CDT-DB, which was started in 1999 and released publicly in 2005, was to systematize spatiotemporal gene expression profiles during postnatal development of mouse cerebellum to help understand the genetic blueprint underpinning brain development.
 BrainTx was started in 2015 with the aim of creating an integrated platform for visualizing and analyzing the genetics that underlie the various stages and states of the mammalian brain. We aim to systematize our original data and the publicly accessible "Big Data" on the brain transcriptome in different stages and states, including time and space, conditions, environment, age, and disease.
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1-2. Privacy Policy
 We will not attempt to collect your personal information when you visit this website; moreover, if you email us, we will respond to your email, but will not otherwise retain or distribute your email address. We provide links to other websites providing additional information about the data compiled in the BrainTx. Once you link to another site, you are subject to the privacy policy of that site.
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1-3. Copyright
 The NIJC, RIKEN-BSI makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either expressed or implied, about the merchantability or fitness of the software or data for a particular purpose. NIJC, RIKEN-BSI makes no claim that the use of this software or data will not infringe on any third-party patents, copyrights, trademarks, or other rights. The software and data, which are provided as-is, are intended to enhance knowledge and encourage progress in the scientific community; they are to be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the NIJC, RIKEN-BSI. We are not responsible for the copyright of any information provided in sites to which we provide links.
Copyright (C) 2005-2017 by BrainTx, NIJC, RIKEN-BSI, Japan. All rights reserved.
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1-4. How to create URL links to the BrainTx
 We recommend that you use the following syntax to create a URL link to the "Gene information page" via NCBI Gene ID (Entrez Gene ID), CD ID number or RefSeq ID.

1) Link to the BrainTx via NCBI Gene ID (Entrez Gene ID)

http://www.cdtdb.neuroinf.jp/CDT/ReferCDInformation.do?geneId=XXXXX

where "XXXXX" is a NCBI Gene ID (Entrez Gene ID).

Example : "Pea15a, NCBI Gene ID (Entrez Gene ID)=18611"

To create a URL link to the gene information page for "18611", put "18611" after "geneId=".

http://www.cdtdb.neuroinf.jp/CDT/ReferCDInformation.do?geneId=18611

2) Link to the BrainTx via CD ID

http://www.cdtdb.neuroinf.jp/CDT/ReferCDInformation.do?cdid=CDxxxxx

where "xxxxx" is a CD ID number.

Example : "Pea15a, CD ID=CD00002"

To create a URL link to the gene information page for "CD00002", put "CD00002" after "cdid=".

http://www.cdtdb.neuroinf.jp/CDT/ReferCDInformation.do?cdid=CD00002

3) Link to the BrainTx via RefSeq ID (or GenBank ID)

http://www.cdtdb.neuroinf.jp/CDT/ReferCDInformation.do?accID=NNNNN

where "NNNNN" is a RefSeq ID (or GenBank ID).

Example : "Pea15a, RefSeq ID=NM_011063"

To create a URL link to the gene information page for "NM_011063", put "NM_011063" after "accID=".

http://www.cdtdb.neuroinf.jp/CDT/ReferCDInformation.do?accID=NM_011063
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1-5. Acknowledgments

 The BrainTx project is supported by the NIJC, RIKEN-BSI. This project is also partly supported by the research grants from the Japan Society for the Promotion of Science (JSPS), the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT), and the Japan Science and Technology Agency (JST). The BrainTx includes many lines of valuable information from the relevant public bioinformatics databases, and contains hyperlinks to these websites. We gratefully appreciate these databases: MGI (Jackson Lab.), Ensembl (Sanger Inst/EBI), NCBI-Nucleotide (NCBI), UniGene (NCBI), NCBI(Entrez)-Gene (NCBI), OMIM (NCBI), GEO (NCBI), KEGG (Kyoto Univ.), Gene Ontology (OBO), Harvester (Karlsruhe Inst. of Tech.), UCSC Mouse Genome Browser Gateway (UC Santa Cruz), GeneNetwork (Univ. of Tennessee), Mouse Phenome Database (Jackson Lab.), BioGPS (Scripps Res. Inst.), STRING (EMBL/SIB/UZH), SynDB (Peking Univ.), Mouse Neuronal Expression Database (NIH), GoPubMed (Technische Univ. Dresden), iHOP (Memorial Sloan-Kettering Cancer Center), PubMed (NCBI), Allen Brain Atlas (Allen Inst. for Brain Sci.), GenePaint (Max Planck Inst.), BGEM (St. Jude children's Res. Hospital), RIKEN Meta Database (RIKEN), FANTOM (RIKEN), BioResource (RIKEN), Molecular Brain Mouse Brain Transcriptome, Affymetrix, Cerebellar Platform (NIJC), Mouse Phenotype Database (NIJC), ViBrism (NIJC), BrainStars (RIKEN), and INCF Japan Node (NIJC).
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1-6. BrainTx Committee

The BrainTx project is supported by the NIJC (the Japan Node of the INCF), JST, JSPS and MEXT.

The Organization of the BrainTx Committee (2017. 4. 1)

Chair:
Teiichi Furuichi (Tokyo University of Science)

Secretary:
Akira Sato (Tokyo University of Science)

Committee members:
Noriyuki Morita (Yasuda Women's University)
Yo Shinoda (Tokyo University of Pharmacy and Life Sciences)
Tetsushi Sadakata (Gunma University)
Michisuke Yuzaki (Keio University)
Takafumi Inoue (Waseda University)
Mitsuhiro Hashimoto (Fukushima Medical University)
Hayato Ohwada (Tokyo University of Science)
Yoko Yamaguchi (Neuroinformatics Japan Center, RIKEN BSI)

Collaborative member:
Hirozumi Nishibe (RIKEN Brain Science Institute)

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1-7. Contact Information

 If you have questions or comments about the BrainTx project or website, please contact us at:

The BrainTx Committee
NIJC, RIKEN Brain Science Institute
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
E-mail: cdt-db@brain.riken.jp
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2. Information about CD genes in BrainTx
2-1. Information about CD genes 

1. CD genes and their identification number (CD ID)
 CD (cerebellar development) genes are initially identified from mouse cerebellum tissue (ICR or C57B/6J) using FDD and GeneChip analyses. Name of "CD" genes has been passed down to BrainTx.
 The CD ID (CD plus five numerals: example CD98765) is the identification number assigned to each CD gene.
 Gene expression data ID (= Parental ID (CD ID) plus sub ID): Multiple different transcripts of the same genes have been identified by employing FDD analysis with different primer sets and microarray analysis with different probes. In addition, multiple different probes, which are derived from different positions of the same gene, can react with either the same transcript or different ones such as alternative splice variants. The BrainTx assigns the parent ID number (= CD ID) to each gene as described above and classifies different expression data for each gene, which are obtained from different transcripts of a gene or obtained by different probes of a gene, as sub ID numbers (gene expression data IDs) that follow the parent ID number.

 Example: CD00001.1 and CD00001.2 mean IDs for two different expression data obtained from the same gene (parent ID = CD00001) and are distinguished from each other by sub IDs ".1" and ".2".
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2. Gene symbol, gene name, alternative name
 We have assigned gene symbols, gene names and alternative names to CD genes by referring to the NCBI(Entrez)-Gene, UniGene, MGI, and Ensembl databases.
 Although a fraction of the ESTs (expressed sequence tags) identified by the FDD analysis do not match any cDNA or EST sequences, but do match known genomic sequences, many of these FDD clones correspond to sequences within introns, 3'-flanking regions, and 5'-flanking regions of known genes. We thus assume that some of these are derived from alternatively spliced mRNAs, differentially terminated or initiated mRNAs, nuclear pre-mRNAs, or noncoding small RNAs. In the BrainTx, such ESTs are provisionally annotated as follows:
Int: within the intron of a corresponding known gene
3'End (predicted): within the 3'-flanking region of a corresponding known gene
5'End (predicted): within the 5'-flanking region of a corresponding known gene
 Here, we restrict the predicted flanking regions within, at most, 2.5 kb from either the 5' or the 3' ends of known genes. Note: Because the FDD-derived, genome-hit CD clones marked with "Int" (intron sequence), "5'End" (5'-upstream sequence), or "3'End" (3'-downstream sequence) are provisional, we leave their gene descriptions up to the judgment of users. These FDD clones might be derived from non-coding RNAs and/or undefined exon sequences that are produced by alternative splicing events during genetic transcription.
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3. Gene category 
 The CD genes are classified into 34 gene categories according to the structural and functional properties of the gene products (encoded proteins), by referring to their annotations in the literature and/or to the terms used to describe them in the MGI and Gene Ontology (GO).

4. Expression profiles   
 Timetabling of gene expression was carried out by developmental RT-PCR, GeneChip, and custom-made cDNA microarray (CDT array) analyses. Cellular mapping of gene expression was conducted by ISH analysis. Brain specificity (tissue distribution) of gene expression was estimated by tissue-specific RT-PCR and GeneChip analyses. The names of mouse strains analyzed (ICR or C57B/6J) are indicated on the expression information pages. Note: Although some digital image data may not be of the highest quality, all data registered here are representative and are the most readily reproducible images we have obtained thus far. Digital images will be updated when improved data are obtained.
 Temporal expression indicates developmental gene expression patterns determined by RT-PCR, GeneChip and CDT array analyses using RNA sources prepared from developing cerebella (RT-PCR and CDT array; E18, P0, P3, P7, P12, P15, P21, and P56) (GeneChip; E18, P7, P14, P21, and P56). Note: Some CD genes that show only slight developmental changes in their expression levels by our conventional semi-quantitative RT-PCR, GeneChip or CDT array analyses are categorized for now into the "almost constant" expression pattern type, since more accurate methods are needed to determine the precise degree of change. The temporal patterns of some genes differ slightly according to the methods used, which may be due to differences in sensitivity between methods or other technical variations.
 Spatial expression indicates cellular and structural expression patterns in cerebellum or hippocampus. Brain distribution indicates regional distribution patterns in brain. They are evaluated by in situ hybridization (ISH) analysis of P7 and P21 mice. Note: ISH images of some CD genes, including even known genes, show nuclear staining patterns (mostly nucleoli), which may be due to hybridization with unspliced RNAs or to unknown causes.
 Brain specificity indicates tissue distribution patterns determined by RT-PCR or GeneChip analyses using RNA sources from eight different tissues. For RT-PCR analysis, RNAs at either P7 or P21, depending on which stage shows a higher expression level, were used, whereas for GeneChip analysis RNAs from mice at both P7 and P21 were used.
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5. EST sequences
 The DNA sequences of all ESTs identified in this BrainTx project were registered to the DNA Data Bank of Japan (DDBJ) and are available by accession number (BP426256-BP428449) from DDBJ/GenBank/EMBL.
6. Links
 The BrainTx includes easy links to relevant bioinformatics database sites. Thus, one can easily access additional information about most CD genes through these links.

Accession ID and EST sequences information: NCBI-Nucleotide. General information: MGI, Ensembl, UniGene, NCBI(Entrez)-Gene, OMIM, GEO, KEGG. Genome information: Harvester, UCSC Mouse Genome Browser Gateway. Functional genomics: GeneNetwork, Mouse Phenome Database, BioGPS, STRING. RIKEN databases: RIKEN Meta Database, FANTOM, BioResource. Nervous system: BrainStars, SynDB, Mouse Neuronal Expression Database, Molecular Brain Mouse Brain Transcriptome. Reference information: GoPubMed, iHOP, PubMed (NCBI). Cellular expression information: Allen Brain Atlas, GenePaint, BGEM. Microarray information: Affymetrix. INCF Japan-Node (NIJC) databases: J-Node Cross-database Search, ViBrism, Cerebellar Platform, Mouse Phenotype Database.
7. References
 To complement the gene annotation information, the BrainTx lists papers selected by us and cited by relevant databases, and contains links to PubMed.
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2-2. Search for CD genes and spatiotemporal gene expression patterns

 In the BrainTx, users can search for CD genes based on gene names/symbols, protein structures, and functions using the Gene Search function. CD genes can be listed based on their specificity in spatiotemporal expression patterns by using the following Expression Data Search Menu, and selected genes may be added to My List (for details about the use of the database, see "Help").
Temporal expression
Temporal expression: Select CD genes based on developmental regulation types. (Press the Legend button for an explanation of abbreviation).

DN: down-regulation C: almost constant expression
UP: up-regulation P: pending classification
UD: up-and-down regulation  
Spatial expression
Spatial expression: Select CD genes based on specifically or dominantly expressed fine structures of cerebellum or hippocampus at P7 and P21. (Press the Legend button for an explanation of abbreviation).

Cerebellum
PM: pia matter PC: Purkinje cell
oEGL: outer EGL (external germinal or granular layer) GC: granule cell
iEGL: inner EGL (external germinal or granular layer) Go: Golgi cell
ML: molecular layer BG: Bergmann glia
PCL: Purkinje cell layer Od: oligodendrocyte
IGL: internal granular layer CN: cerebellar nuclei (deep cerebellar nuclei, DCN)
WM: white matter As: astrocyte
St: stellate cell other: other cell
Ba: basket cell  

Hippocampus
CA1: CA1 As: astrocyte
CA2: CA2 Od: oligodendrocyte
CA3: CA3 Mg: microglia
DG: dentate gyrus other: other cell
IN: interneuron  
Brain distribution
Brain distribution: Select CD genes by specifically or dominantly expressed brain regions at P7 and P21. (Press the Legend button for explanation of abbreviation).

Ob: olfactory bulb Tc: tectum
Cx: cerebral cortex Tg: tegmentum
Bg: basal ganglia Cb: cerebellum
Hi: hippocampus Po: pons
Th: thalamus Me: medulla oblongata
Hy: hypothalamus Other: other region
Brain specificity
Brain specificity: Select CD genes by brain specificity or dominancy in comparison with seven other tissues (thymus, lung, heart, liver, spleen, kidney, testis) at P7 or P21. (Press the Legend button for an explanation).

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3. Information about the gene expression profiling data
"Experimental Information" can be downloaded from the menu "Download" option in the menu bar.

The data obtained by developmental time series GeneChip analysis (Publication-3, Kagami and Furuichi, 2001) are also available in the NCBI Gene Expression Omnibus (GEO) (Platform GPL8, Series GSE2, and Sample GSM50, GSM51, GSM52, GSM53, and GSM54).
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4. Publications
1)   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
  
2)   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
  
3)   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
  
4)   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
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Copyright (C) 2005-2017 by BrainTx, NIJC, RIKEN-BSI, Japan. All rights reserved. Updated: April 1, 2017. Ver.5.2