Contents

Necessary conditions for use of the BrainTx

  • Macintosh
    Mac OSX 10.4 or higher: Safari 10 or higher, Firefox 52 or higher
  • Windows
    Windows 7/8/8.1/10: Internet Explorer 7-11, Microsoft Edge, Firefox 52 or higher
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Search Menu

Click on the appropriate icon or term to access gene information and expression data.

Note: Selection of only one icon or term from the list of search items below is acceptable.
Then, click on Search. To clear the search item, click on Clear.
To restart your selection, click on Reset.
A search can be executed by selecting multiple search items simultaneously.
The following search items are available.


Top page
"Quick Search"
    Select a search item by clicking "tab"
  • - Keyword/Gene tab
  • - Brain distribution tab
  • - Brain specificity tab

"J-Node Cross-database Search"
Enter keywords, gene names or IDs in the search box, and then click on Search to access the search result page by execution of "J-Node Cross-database Search" on the "INCF Japan Node" website.

Advanced Search page
Select the Search Mode: "Brain region" and "Target genes".

"Brain region"
All: You can search for the expressed genes in any region of the brain by utilizing search items ("Gene Name & Keyword Search", "Gene ID Search", "Brain distribution search", or "Brain specificity search").
Cerebellum: In addition to search items in above "All" region mode, you can search for the genes with the more detailed data for spatial or temporal gene expression information of cerebellum by utilizing search items ("Spatial expression search", "Temporal expression search", or "Expression peak stage search").
Hippocampus: In addition to search items in above "All" region mode, you can search for the genes with the more detailed data for spatial or temporal gene expression information of hippocampus by utilizing search items ("Spatial expression search", "Temporal expression search", or "Expression peak stage search"). Note: Search items ("Temporal expression search" and "Expression peak stage search") in "Hippocampus" region mode cannot be utilized as of now.

"Target genes"
All genes: You can search for all registered genes that are mainly composed of genes on the Affymetrix GeneChip Mouse Genome 420 2.0 Array.
Differentially expressed genes: You can search for the genes differentially expressed during development in all registered genes.

"Gene Search" (see 4. Gene Search)
 - Gene Name & Keyword Search
 - Gene ID Search

"Expression Data Search" (see 5-9. Expression Data Search)
 - Spatial expression (in Cerebellum or Hippocampus mode)
 - Temporal expression (in Cerebellum or Hippocampus mode)
 - Expression peak stage (in Cerebellum or Hippocampus mode)
 - Brain distribution
 - Brain specificity

 A query composed of multiple search items (a combination of items from both Gene Search and Expression Data Search) described above can be executed.
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Search Menu legends

 Click on Legend in each search item to open the Legend page, which explains the icons and abbreviated terms.

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Gene Search

 "Gene Search" can be performed by choosing "Search Mode" (Brain region: "All" or "Cerebellum" or "Hippocampus") (Target genes: "All genes" or "Differentially expressed genes"). A query combining "Gene Search" with "Expression Data Search" can be performed.

 Gene Name & Keyword Search: Type more than two letters or numbers to activate. Query targets are gene symbol/name (description) (e.g., glur1, glutamate) and protein structure/function (for example, PDZ, synapse). Multiple word searches can be executed by using the AND function; that is, by entering a space between keywords (for example, AMPA receptor).

 Gene ID Search: Type number (numerals) of the NCBI(Entrez) Gene ID or CD ID (parental ID [e.g., 00001] or parental ID plus sub ID [e.g., 00001.2]). Only one ID number can be queried at a time.
For explanation on "Parental ID" and "sub ID", please open "About" page and see "2-1. Information about CD genes".

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Expression Data Search- spatial expression

 "Expression Data Search" can be performed by choosing "Search Mode" (Brain region: "All" or "Cerebellum" or "Hippocampus") (Target genes: "All genes" or "Differentially expressed genes"). A query combining "Expression Data Search" with "Gene Search" can be performed.

 CD genes can be searched for spatial (cellular and structural) expression patterns obtained by in situ hybridization (ISH) analysis. Spatial expression patterns in sagittal sections of P7 and P21 cerebellum or hippocampus are classified by the structures and major cell types in which CD genes are expressed, as follows:


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

Hippocampus
CA1: CA1
CA2: CA2
CA3: CA3
DG: dentate gyrus
IN: interneuron
As: astrocyte
Od: oligodendrocyte
Mg: microglia
other: other cell
1. Click on the gene expression type button: either "all expression" or "characteristic expression".
 
all expression: Search for all genes that are expressed, regardless of their expression levels and/or patterns, in the selected cell type or structure.
 
characteristic expression: Search for the genes that are characteristically, strongly or specifically expressed in the selected cell type or structure.
 
Note: This selection is effective only for a spatial expression search.
2. Select a structure or cell described above, and then click on the Search button.
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Expression Data Search- temporal expression

 "Expression Data Search" can be performed by choosing "Search Mode" (Brain region: "All" or "Cerebellum" or "Hippocampus") (Target genes: "All genes" or "Differentially expressed genes"). A query combining "Expression Data Search" with "Gene Search" can be performed.

 CD genes can be searched for temporal (developmental time series) expression patterns obtained by RT-PCR, GeneChip and CDT array analyses. Temporal expression patterns in the developing cerebellum or hippocampus (E18-P56) are classified into five types, indicated by the following abbreviations:

1. DN (down): down-regulation
2. UP (up): up-regulation
3. UD (up-and-down): up-and-down regulation
4. C (almost constant): almost constant expression
5. P (pending): pending classification
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Expression Data Search- expression peak stage

 "Expression Data Search" can be performed by choosing "Search Mode" (Brain region: "All" or "Cerebellum" or "Hippocampus") (Target genes: "All genes" or "Differentially expressed genes"). A query combining "Expression Data Search" with "Gene Search" can be performed.

 CD genes can be searchable for expression peak stages obtained by RT-PCR, GeneChip and CDT array analyses. Expression peak stages are classified into the following five types defined by the postnatal week when the highest expression levels are observed from among the stages indicated in parentheses.

1. 0wk: postnatal first day (highest at E18-P0)
2. 1wk: postnatal first week (highest at P3-P7)
3. 2wk: postnatal second week (highest at P12-P15)
4. 3wk: postnatal third week (highest at P21 or so)
5. 8wk: postnatal 8th week (highest at P56 or so)
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Expression Data Search- brain distribution

 "Expression Data Search" can be performed by choosing "Search Mode" (Brain region: "All" or "Cerebellum" or "Hippocampus") (Target genes: "All genes" or "Differentially expressed genes"). A query combining "Expression Data Search" with "Gene Search" can be performed.

 CD genes can be searched for brain distribution patterns obtained by ISH analysis. Regional distribution in sagittal sections of P7 and P21 brains is defined according to the specificity or characteristics of gene expression patterns, as follows:

  1. Ob: olfactory bulb
  2. Cx: cerebral cortex
  3. Bg: basal ganglia
  4. Hi: hippocampus
  5. Th: thalamus
  6. Hy: hypothalamus
  7. Tc: tectum
  8. Tg: tegmentum
  9. Cb: cerebellum
10. Po: pons
11. Me: medulla oblongata
12. Other: other region
1. Click on the gene expression type button: either "all expression" or "characteristic expression".
 
all expression: Search for all genes that are expressed, regardless of their expression levels and/or patterns, in the selected region.
 
characteristic expression: Search for the genes that are characteristically, strongly or specifically expressed in the selected region.
 
Note: This selection is effective only for brain distribution searches.
2. Select one of the brain regions named above and click on the Search button.
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Expression Data Search- brain specificity

 "Expression Data Search" can be performed by choosing "Search Mode" (Brain region: "All" or "Cerebellum" or "Hippocampus") (Target genes: "All genes" or "Differentially expressed genes"). A query combining "Expression Data Search" with "Gene Search" can be performed.

 CD genes can be searched for brain specificity (tissue distribution) patterns obtained by RT-PCR and GeneChip analyses. Tissue distribution (brain, thymus, lung, heart, liver, spleen, kidney and testis) of gene expression in P7 or P21 mice is defined as follows:

1. Brain-specific: Gene expression is specific to the brain, and is barely or not at all detected in the other tissues.
2. Brain-dominant: Gene expression is dominant (or relatively high level) in the brain in comparison with other tissues.
3. Ubiquitous: Gene expression is present at a low level in the brain and is ubiquitous or widespread in many tissues.
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Search results

Search result page shows a gene list of hits in alphabetical/numerical order of CD ID, accession number, gene symbol and name, icons for gene information, link information of relevant bioinformatics websites, temporal expression, spatial expression, tissue expression (brain specificity), and gene category information pages, as shown below (note that if no data are available, no corresponding icon will be displayed):

1. Search Mode: Brain region ("All" or "Cerebellum" or "Hippocampus") and Target genes ("All genes" or "Differentially expressed genes") selected for your search. Input Search Terms: Your query.

2. Items: The number of total hits is shown. Results pages to display can be changed by clicking on the "First" (first page), "Prev" (previous page), "Next" (next page) or "Last" (last page) button.

3. Show: The number of hits displayed on the Search Results page can be 10, 20, 50, or 100 (default: 20) (select number and then press Change).

4. Sort by: Genes on Search results pages can be sorted by "Gene Symbol" or "CD ID" and the alphabetical and numerical order is changeable by selecting "up" and "down" buttons. To sort genes according to "Temporal information", "Spatial information", "Tissue information", or "Gene category information" data on the top of your list, select one of these terms from the pull-down sort menu.

5. Add to My List: If you wish to place an item in My List, click on the box beside it to select it, and then click on Add to My List (for more on the My List function, see below). The Check All and Uncheck All buttons allow you to check all items and to clear all checks on the currently opened page, respectively.

6. Print version: To create a print-ready window of the Search Results page, click on Print version. Use your browser's print menu to print all result records.

7. Result Download: To download a CSV format file containing search results, choose a file size (small or normal) and then click on Download.

8. CD ID: Link to the Gene information page. Click on CD ID to open a detailed information page for each hit gene.

9. Accession No.: Click on accession number to access the corresponding NCBI-Nucleotide information web pages.

10. Gene Information: Click on the "information" icon to open the Gene information page.

11. Links: Mouse over the "chain" icon to display the link launcher of the relevant bioinformatics websites (NCBI Gene, MGI, GEO, Allen Brain Atlas, GenePaint, ViBrism, BrainStars, BioGPS, Mouse Phenotype DB, INCF J-Node Cross-DB, RIKEN Meta DB). Click the website icon or name to access to the corresponding gene information page of the selected website.

12. Temporal: Mouse over the "clock" icon to display the dropdown menu of brain regions, and subsequently mouse over the selected brain region to display the dropdown menu of CD ID plus sub IDs. When multiple sub IDs are present, IDs having the data are highlighted. Select an ID number to open the Temporal information page.

13. Spatial: Mouse over the"brain" icon Spatial icon to display the dropdown menu of CD ID plus sub IDs. When multiple sub IDs are present, IDs having the data are highlighted. Select an ID number to open the Spatial information page.

14. Tissue: Mouse over the "mouse" icon Tissue icon to display the dropdown menu of CD ID plus sub IDs. When multiple sub IDs are present, IDs having the data are highlighted. Select an ID number to open the Tissue information (Brain specificity) page.

15. Category: Click on the "set" icon Category icon to open the Gene category information page.

16. Show Graph: To display temporal expression graphs of hit genes, click either GeneChip Graph or CDT array Graph.

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Gene information

Click on a CD ID or Gene Information icon on any page of the BrainTx to open the Gene information page containing detailed gene information as follows.

1 CD ID Identification number of CD gene
2 Gene Symbol Symbol of gene name (NCBI)
3 Gene Name Full gene name (NCBI)
4 Alternative name(s) Alternative gene names
5 Accession ID Accession number with hyperlink to the NCBI-Nucleotide website
6 Gene Category Gene category name by classification based on gene function
7 Gene Ontology Gene ontology terms with hyperlinks to the gene list page with the selected gene ontology term
8 Temporal expression Temporal expression pattern type
9 Spatial expression Cellular and layer localization
 *Characteristic regions and sites are underlined.
10 Brain distribution Brain regional distribution
 *Characteristic regions and sites are underlined.
11 Brain specificity Brain specificity pattern type
12 Experimental data
  • Temporal (RT-PCR, GeneChip and CDT array data)
  • Spatial (ISH brain image data)
  • Tissue (RT-PCR and GeneChip data)
  • Category (gene categories and graphs)
*To see the experimental data, click on the icon. When multiple sub IDs are present, IDs having the data are highlighted.
13 Probe
  • CDT EST: Accession numbers of CD clones (ESTs) with hyperlinks to NCBI-Nucleotide.
  • Affymetrix: GeneChip Array probe ID with hyperlink to the Affymetix website.
14 Links Hyperlinks to the relevant bioinformatics websites (NCBI(Entrez)-Gene, MGI, Ensembl, UniGene, OMIM, GEO, KEGG, Harvester, UCSC MGBG, GeneNetwork, MPD, BioGPS, STRING, BrainStars, SynDB, MNED, GoPubMed, iHOP, PubMed, Allen Brain Atlas, GenePaint, BGEM, RIKEN Meta Database, FANTOM, BioResource, Molecular Brain Mouse Brain Transcriptome, INCF Japan-Node Cross-database Search, ViBrism, Cerebellar Platform, Mouse Phenotype Database)
15 References References with hyperlinked PubMed IDs
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Temporal information

 Temporal (developmental time series) expression profile data obtained by developmental RT-PCR, GeneChip and CDT array analyses are compiled. Mouse strain information is shown (ICR or C57B/6J). When multiple sub IDs are present, IDs having the data are highlighted. Click CD ID to open an information page.

 Note: Since three methods (RT-PCR, GeneChip and CDT array) utilize different types of probes (PCR primers, short synthetic nucleotides, or EST sequences) and different positions of a gene as probes, expression data obtained by these methods often differ from one another due to detection of alternative splice variants. Thus, expression patterns shown in "Temporal information page" are sometimes different among the methods or sub IDs.

1. Developmental RT-PCR

 Representative agarose gel banding patterns of conventional semi-quantitative RT-PCR products are shown. An example of the experimental conditions used is indicated. You may be required to optimize this condition, but this probably depends on the experimental apparatus and reagents you use.

2. GeneChip

 A graph and table indicate normalized signal values (bars, y-axis shown in right) and relative values (%) (circles, y-axis shown in left) of gene expression during developmental stages. The maximum signal values of right y-axis can be adjustable by selecting from 10000, 5000, 1000, 500 and 100. "Peak" indicates the stage with the highest intensity. Experimental conditions are indicated: Affymetrix Probe ID, GeneChip array and signal range (maximum and minimum values).

3. CDT array

 A graph and table indicate normalized signal values (bars, y-axis shown in right) and relative values (%) (circles, y-axis shown in left) of gene expression during developmental stages. The maximum signal values of right y-axis can be adjustable by selecting from 20, 10, 5 and 2.5. "Peak" indicates the stage with the highest intensity. Experimental conditions are indicated: Signal range (maximum and minimum values).

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Spatial information

 Spatial (cellular and structural) expression profile data obtained by ISH histochemistry of sagittal brain sections at P7 and P21 are compiled. Mouse strain information is shown (ICR or C57B/6J). When multiple sub IDs are present, IDs having the data are highlighted. Click CD ID to open a viewer page.


Note:Since the method utilizes different positions of a gene as probes, expression data obtained by these probes often differ from one another due to detection of alternative splice variants. Thus, expression patterns shown in "Spatial information page" are sometimes different among the sub IDs.

Detailed viewer

 Click a brain image at P7 or P21 to open a detailed image viewer window.

 Gene information box: A box at the top indicates the CD ID, gene symbol and developmental stage.

 Tool bar: A tool bar on the left is used to operate a brain image in a view window: move up/down and left/right, magnify by moving the slider bar or by using the loupe icon (+/-, magnification/reduction), move by hand icon.

 Image mode: A display image can be chosen from three modes: Color, Gray and Inverted modes.

 Display area: A frame is the brain area showing in a view window, and can freely be moved by clicking and dragging.

 Scale bar: Scale bar of magnified brain images is indicated.

Extra Data

 Extra data provide ISH images of brain subregions and characteristic expression patterns in brain, etc.
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Tissue information (brain specificity)

 Tissue expression profile (brain specificity) data obtained by tissue-specific RT-PCR and GeneChip analyses are compiled. Mouse strain information is shown (ICR or C57B/6J). When multiple sub IDs are present, IDs having the data are highlighted. Click CD ID to open an information page.

Note: Since two methods (RT-PCR and GeneChip) utilize different types of probes (PCR primers or short synthetic nucleotides) and different positions of a gene as probes, expression data obtained by these methods often differ from one another due to detection of alternative splice variants. Thus, expression patterns shown in "Tissue information page" are sometimes different among the methods or sub IDs.

1. Tissue-specific RT-PCR

 A representative agarose gel banding pattern is compiled from RT-PCR analysis of brain specificity or dominancy of gene expression among eight different mouse tissues (brain, thymus, lung, heart, liver, spleen, kidney, and testis) at either P7 or P21, with a higher expression level in the cerebellum. The experimental conditions used are also described here. Mouse strain information is shown (ICR or C57B/6J).

2. GeneChip

 A graph and table indicate normalized signal values (bars, y-axis shown in right) and relative values (%) (circles, y-axis shown in left) of gene expression in eight different tissues of P7 and P21 mice (C57B/6J). The maximum signal values of right y-axis can be adjustable by selecting from 10000, 5000, 1000, 500 and 100. Experimental conditions are indicated: Affymetrix Probe ID, GeneChip array and signal range (maximum and minimum values).
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Gene Ontology search function

 CD genes can be searched for Gene Ontology (GO) terms.

1. GO Tree Browser

 Click a GO term. CD genes classified into the selected term are shown in the hierarchical tree of GO (biological process, cellular component and molecular function).

2. GO Term Search

 CD genes can be searched by gene name/symbol, GO terms, NCBI(Entrez) Gene ID, or CD ID. Hit genes are shown in the GO hierarchical tree, so that a correlation among hit genes is estimated.
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Gene category and "Gene expression graph" function

 Gene category information on CD genes is compiled. CD genes are categorized into 34 categories, basically by their functional properties. Temporal expression profiles (plots of GeneChip and CDT array data) of genes registered in each category can be displayed graphically.

Note: Some CD genes are categorized into more than one category because of their multiple functional properties.

Note: How to display Gene Category graph on your computer.
  1. Install the "Java" to your computer (En/Ja).
      (The Java installer for Windows and Mac OS can be obtained from the Java web site.)
  2. For Google Chrome and Firefox users, use a different web browser (Internet Explorer, Safari, etc.).

1. Click on the Gene Category tab of the top menu bar to open the full gene category page.
The number of genes registered in each category is indicated.

All: Number of all genes registered.
GeneChip: Number of genes whose GeneChip data are available.
CDT array: Number of genes whose CDT array data are available.
2. Gene category graph: Click on the graph button to open the Gene category graph display page.

3. Click on the check box next to a gene to show its associated expression graphs.

4. Click on the red bar of a peak stage to show graphs of genes that peak at that stage.

5. Click on the info button to open the Gene information page of the corresponding gene.
* When multiple sub IDs are assigned to the same gene, GC graph data for each sub ID are accessible from the "Gene information page".
6. Click on the line graph to display the corresponding gene description in the bottom rectangular window.

7. Click on the Add to My List button to add the displayed gene description to your My List page.

8. Click on the Select All and Release All buttons to choose all entry genes and to reset all selections, respectively.

9. Each page displays a list of up to 200 genes within a category. More than 201 genes are shown on multiple pages. The previous "<<" and next ">>" buttons are used to open the previous and next pages, respectively.

10. The order of genes in a list window can be changed in either "alphabetical" or "CD ID"

11. Graph display mode (Grouping of gene expression by): Expression plots in a graph window can be selected by two view modes ("peak stage" or "pattern type"). Choose and then press Reload.

Peak stage: Click a red peak stage bar (GeneChip graph: E18, P7, P14, P21, or P56; CDT array graph: E18, P0, P3, P7, P12, P15, P21, or P56) to display plots of genes with the selected peak stage.
 
Pattern type: Click a red temporal expression pattern bar (up, down, up-and-down, almost constant, or pending) to display plots of genes with the selected expression pattern.
12. Graph display mode (Select vertical (y) axis): The y-axis of graph can be chosen from "relative value (%)" or "signal value". Choose and then press Reload. In "signal value" mode, "maximum value" is selectable from four grades 10000, 5000, 1000 and 500 on GeneChip graph and four grades 20, 10, 5 and 2.5 on CDT array graph.

13. Description flame: Click a graph line to display the gene name in this flame.


*Note: If you select a category that has over 200 records, it may take a few minutes to draw the graph.
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My List function

 You can select CD genes that are hits with your query and transfer them to your My List page, thus creating a list of selected genes. This listing operation can be executed repeatedly, so that you can compile one composite list of CD genes selected on multiple query tasks. The My List page is basically displayed in the same format as the Search Results page except for the following two functions:

1. Delete All: Reset function to remove all genes on your My List page (press Delete All button).

2. Show My Graph: Graphical display of GeneChip and CDT array data of genes on your My List page.

 You can access the gene detail and spatiotemporal expression information pages from the My List page as well. Your list can be sorted by Gene symbol, CD ID, Temporal information, Spatial information, Tissue information, or Category information. To download a CSV format file containing your search results, select a file size (small or normal) and then click on Download. To create a print-ready window of the Search Results page, click on Print version. Use your browser's print menu to print all result records.

Note: Your "favorite" gene list registered on the My List page is used only during a single browser session; it expires when you quit your browser. However, you may be able to regain use of your list by re-accessing the BrainTx website during a single browser session, even if you have previously quit the BrainTx website. If you need a record of your list, download or print it by using the Download and Print version buttons, respectively (see the "Search results" section).

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ISH Atlas

 The ISH Atlas is composed of two atlases of developing mouse brains, with small collections of data on representative ISH staining and histochemical staining for easy reference.

1. Gene Expression Brain Atlas: ISH staining patterns of cell marker genes. Click on Subregion/cell type to see the ISH page, and CD ID to open the Gene information page.

2. Developing Mouse Brain Atlas: Histochemical (cresyl violet and luxol fast blue) and immunohistochemical (specific antibodies) staining patterns of developing mouse brains. Click on Stage to open the staining page.
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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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Copyright (C) 2005-2017 by BrainTx, NIJC, RIKEN-BSI, Japan. All rights reserved. Updated: April 1, 2017. Ver.5.2