Viewing Gene Expression Data

The mouse brain atlas offers the following ways for you to find gene expression data:

• Use Gene Search to locate genes' data by name, symbol, NCBI accession number, MGI Marker, Unigene Cluster ID, or Entrez Gene ID
• Search for genes by anatomic region and expression level using Anatomic Search
• Search for genes data based on Fine Structure Annotation
• Search at a granular level using Boolean operators on specific field names using the Boolean Syntax Query
• Download a comma delimited list of all genes with expression data

Gene Search

Search for a specific gene by name, symbol, NCBI accession number, or Entrez gene ID by typing the gene name in the text box on the Gene Search tab at the top of the Brain Atlas page. As you type, the application displays below the text box a selectable list that contains genes that match your search string to that point. Select an item from the list and click the "Search" button. The results are displayed in a list that shows all genes with expression data that match your query.

Tips for searching:

• If you are unsure of spelling, begin typing the gene identifier and suggestions will be offered.
• Include an asterisk (*) as a wildcard character before or after your search text to return genes that start with or end with that text. For example, enter pig* to return genes that start with pig or *pig to return genes that end with pig.
• If you do not include an asterisk (*) wildcard character, wildcards are implied to surround your search text. So if you search using the text pig, for example, you'll get results that include pig anywhere within the gene name or symbol.
• Select the "Show Exact Search Results Only" check box to remove the implied wildcards. This is useful if you want to return only those genes that exactly match your search text.
• Place the search text within quotes to include spaces or special characters.
• When searching for more than one gene, separate each search term by a comma, semicolon, or line break (if in bulk query view).
• Click the "Input Bulk Query" button to search for many genes at once. Doing so expands the text box, making it easier to copy and paste a list of genes from a text file or spreadsheet. Note that a bulk query behaves differently than a single gene query in two ways. The first difference is that this type of query does not search the genename field. Secondly, the bulk query does not implicitly include wildcard characters around your search text (you must specify them).

Anatomic Search

Use the Anatomic Search option to search for gene expression data that is processed and stored within the ABA database by restricting your search to a specific anatomic region, an expression intensity level, expression density, and the pattern exhibited by the gene expression. Optionally, add additional search criteria using the Boolean operators And or Or to expand your search to additional anatomic regions.

An anatomic search returns a subset of genes that meet your specified search parameters; however, anatomic search does not return a comprehensive list of genes with a given expression profile for the entire database. Use Anatomic Search as a general guide to search for gene series that are expressed in a particular region, but not in lieu of other empirical methods for detecting gene expression (such as microarray analyses).

To build an anatomic search:

1. Select the "Anatomic Search" radio button
2. Select the search parameters from the following lists:
   • Anatomic Regions: the region of the brain in which you want to search.
   • Expression Level: choose from among Any, Low/Medium, and High for the level of gene expression in the returned samples.
   • Expression Density: choose from among Any, Low/Medium, and High for the density of gene expression in the returned samples.
   • Expression Pattern: choose from among Any, Not Clustered, and Clustered for the pattern of the expression in the returned samples.
3. If you would like to expand your search to additional anatomic regions, click "Add Row," select an And or an Or Boolean operator and enter additional search parameters. You can search using a maximum of three anatomic parameters. Click "Delete" to the right of the secondary search parameter to remove it from the search criteria.

Fine Structure Annotation

Select a structure to return genes found to have a high level of expression in it. For more information on the methods use to generate the annotations, refer to the user guide.

Boolean Syntax Query

Use a Boolean Syntax Query to create a custom query of the Brain Atlas database. This is done by composing query phrases that target specific database fields. You can use the Boolean operators and as well as or to link together query phrases-and parentheses to control query flow-to refine your search by specifying exactly which fields to search for or not to search for in the database.

Include characters reserved as operators (such as "<") or spaces in your search by surrounding your search text by quotation marks (" "). For example, surround your search text with quotes if searching the mgi field for a specific Mouse Genome Informatics (MGI) ID (each of these IDs contain a colon).

Searchable Fields

Field	Description	Example
altgenesym	Gene alias	Dsh
chr	Chromosome number	5
entrezgeneid	Entrez (NCBI) GeneID (including former LocusLink LocusIDs)	20423
genename	Gene name	sonic hedgehog
genesymbol	Gene symbol, including a select few unofficial symbols and aliases (use altgenesym to search on additional gene aliases)	Shh
gensatid	Gensat ID	380
hid	Homologene ID	30961
mgi	Mouse Genome Informatics (MGI) ID (surround your search text by quotes if it includes a colon, which is standard to MGI IDs)	"MGI:98297"
polypeptide	Swiss-Prot accession number	Q62226
refseq	Accession of NCBI reference sequences (RefSeqs), nucleotides only	NM_009170
imageseries	Image series ID	75749418
structac	Structure acronym, defined as follows: Cerebellum = CB Cerebral cortex = CTX Hippocampal formation = HPF Hypothalamus = HY Medulla = MY Midbrain = MB Olfactory bulb = OLF Pallidum = PAL Pons = P Striatum = STR Thalamus = TH	CB
unigenecid	UniGene cluster ID	Mm.57202
xdensity	Gene expression density, which must be used as a sub-criterion of structac: No expression density is equal to 0 Low/medium expression density is equal to 1 High expression density is equal to 2 Indicate density inside square brackets. Use the format "structac=HY[xdensity=2]". If used in conjunction with xlevel and/or xpattern, use a semicolon ";" to separate each criterion.	structac=My[xdensity=1]
xlevel	Gene expression level, which must be used as a sub-criterion of structac: No expression level is equal to 0 Low/medium expression level is equal to 1 High expression level is equal to 2 Indicate expression level inside square brackets. Use the format "structac=HY[xlevel=1]". If used in conjunction with xdensity and/or xpattern, use a semicolon ";" to separate each criterion.	structac=My[xlevel=2]
xpattern	Pattern of gene expression, which must be used as a sub-criterion of structac: Unclustered expression is equal to 1 Clustered expression is equal to 2 Indicate the expression pattern inside square brackets. Use the format "structac=CB[xpattern=1]". If used in conjunction with xdensity and/or xlevel, use a semicolon ";" to separate each criterion.	structac=CB[xpattern=2]

Boolean operators

Operator	Description
AND	Returns data that matches both conditions
OR	Returns data that matches either one of the conditions
( )	Use parenthesis to change the order of evaluation of search criteria

Equality operators

Operator	Description
=	Matches exactly
~	"Contains," "starts with," or "ends with" when criteria is combined with an asterisk (*) wildcard character, which is substituted for zero or many characters.
>	Greater than
<	Lesser than
!=	Not equal to
!~	"Does not contain," "does not start with" or "does not end with" when the criteria is combined with the asterisk (*) wildcard character.

Example queries

Query	Description
genesymbol=Bach2	returns a list of image series for the Bach2 gene.
genesymbol=Bach2 or genesymbol=Sod1	returns the image series for Sod1 (superoxide dismutase 1, soluble) as well as the image series for Bach2.
genesymbol~Syt*	returns all image series where the gene symbol starts with Syt (synaptotagmins). Notice the use of the wildcard character (*) after the Syt in combination with the "~" operator.
genename="sonic hedgehog"	returns the image series for the gene name sonic hedgehog. Note the use of quotes ("") around the search text to support the inclusion of a space.
mgi~"MGI:98*"	returns the image series for all Mouse Genome Informatics (MGI) IDs that start with MGI:98. Note the use of the wildcard to specify that the IDs should start with MGI:98 and the use of quotes around the search text-this time to support the inclusion of a colon (:) character, which is still recognized as an operator.
genename~*phosphate*	returns a list of image series similar to the first example for the keyword search. With the wildcard character (*) both before and after the criteria, this query will return all gene names that contain phosphate.
structac=HY[xlevel=2]	returns a list of image series that feature a high level of expression in the Hypothalamus region. Note that the "xlevel" search parameter is a sub-criterion of structac, as indicated by the square brackets [ ].
structac=HY[xlevel=2;xdensity=1;xpattern=2]	adds to the previous example to further filter the results to those with a clustered pattern of gene expression.
structac=HY[xlevel=2;xdensity=1;xpattern=2] and genename~*protein*	adds to the previous example example by restricting the anatomic search so that it only returns genes that contain the string protein in the gene name.
imageseries=71247618	returns the gene associated with the imageseriesid specified.

Viewing Search Results

A list of genes that match your criteria are returned as the search results. The columns include:

Column	Description
Experiments	Click the plus button (+) to display the sagittal and/or coronal image series associated with that gene.
Gene Name	Genes with ISH image series will have a processing status of "Available." Click the gene name to display the sagittal and/or coronal image series associated with that gene.
Gene Info	Click the gene symbol to open a new window with additional gene metadata
Processing Status	Available: sagittal and/or coronal ISH image series are available Coming soon: probe succeeded and the experiment is in process Design failed Design untried Probe failed
Links	Related Web sites
Related Data	Links to additional Allen Institute projects that have data for the gene or its orthologs

Gene rows with a processing status of "Available" can be expanded to show image series associated with the gene. The columns include:

Column	Description
Select	Add the image series to "Your Selections." The selected image series can be opened in the Multiple Image Viewer or you can view the thumbnails.
Image Series	Click the Image Series ID to open a new window with additional metadata regarding the experiment.
Gene Sym	Gene symbol
Plane	Sagittal or Coronal
Orientation	Probe orientation with values of sense or antisense
3D Data	3D expression volume file that can be opened by Brain Explorer
Expression Summary	Graph showing gene expression density and level in structures
NeuroBlast	Find genes with a similar expression profile in the selected structure