h2. Microarray Data

For those who are arriving at this database without a prior knowledge of genetics or specific genes, a search for a gene category by disease, pathway, cell type or function, click on the relevant search term in the        tag cloud may be of most initial use.        

The website offers three types of searches to allow a user to:     (1) obtain gene expression data for specific genes (or probes) of interest [(Gene Search)|#Gene Search];     (2)  compare expression between different anatomic regions [(Differential Search)|#Differential Search]; and     (3) use a 'seed' gene to find other genes with similar expression patterns [(Find Correlates)|#Correlative Search].
 


h3. Gene Search

To search for probes associated with a specific gene or group of genes,        select the Gene Search radio button and type the gene name, gene symbol Entrez Gene ID or probe ID in the search box        (multiple genes searches require an OR between gene names) before clicking the "Search" button.


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!ALLEN Human Brain Atlas^HBA_landing_page.jpg|border=1!

h4. Boolean Syntax

The following special operators can be used to build queries:
|| Operator || Example Search Type || Example Query ||
| AND operator: & | Gene | [dopamine & receptor|http://human.brain-map.org/search.html?query=dopamine+%26+receptor&type=microarray] |
| OR operator: \| | Gene | {menulink:custom|link=http://human.brain-map.org/search.html?query=ABAT+%7C+ACHE&type=microarray|target=_blank}ABAT\|ACHE{menulink} |
| NOT operator: \! | Gene | ["dopamine receptor" \!DRD3|http://human.brain-map.org/search.html?query=%22dopamine+receptor%22+%21DRD3&type=microarray] |
* AND, OR and NOT may be used in place of their corresponding operators. They must be upper case.
* The AND operator (&) is implicit, so spaces between words  that are not separated by an operator will be treated like an &.
* OR (\|) has higher operator precedence than AND (&).
* Parentheses can be used to group criteria, but nested parentheses are not supported at this time.
* The NOT operator (\!)is not supported within parentheses.





h3. Differential Search

Another common usage of gene expression databases is to find genes that show enrichment of       expression in one region compared to another region. This type of query is supported by the Differential Search mode. Select the "Differential Search" radio button. To find genes or       probes with an enhanced gene expression profile in one or more brain regions when compared to one or more other brain regions, enter the       target structure in the top search box (separate structures with a semicolon) and your contrast structure(s) in the bottom search box and       click on the Search button.





!differential_search.jpg|border=1!






Your search will return differentially expressed genes displayed only for the brain regions selected. The results will show genes exhibiting higher       expression in the target region(s) compared to the contrast region(s). (To view the expression patterns       of the returned probes throughout the entire brain, turn off the "Restrict Domains" function below the       heat map.) Search results are sorted either by p-value or fold change, indicated by the arrow on       the buttons over the column of genes. To alter the sort parameter, click on either the "p value" or       the "fold-change" buttons.


!diff_sch_results.jpg|border=1!

To perform the previous search in reverse, click the toggle button to the left of the Search button.















h3. Correlative Search

In using gene expression databases, a "search by example" feature is also highly desirable 	  as genes with similar expression patterns may be related in function. The Find Correlates search       utility will accomplish this function. This search by example facility is also available 	  in the Allen Mouse Brain Atlas, Allen Developing Mouse Brain Atlas and the BrainSpan atlas of the developing human brain.

!ALLEN Human Brain Atlas^Find_correlates.jpg|border=1!

Once you have identified a gene of interest in the Atlas, to find other genes with spatial expression profiles similar to your gene of interest, first select your probe by       clicking on any cell in the heat map related to that probe. You will see that probe listed in the       box above the right hand side of the heat map. Then select the brain structure(s) in which you       would like to see a similar expression pattern, and click "Find Correlates". This action will return       probes with a similar expression profile to brain region(s) in which you are interested.


!ALLEN Human Brain Atlas^restrict_domains.jpg|border=1!



Only       regions selected for the search will be displayed. To see the search results across the entire brain,       turn off the "Restrict Domains" function at the bottom of the heat map.
You can see "anti-correlated" returns by toggling the sort order on column "r" or scrolling       to the bottom of the heatmap.








h3. Data Visualization

Based on your search, the resulting microarray data sets are presented as a matrix with brain         structure (by individual donor) on the horizontal x-axis and gene probes on the vertical y-axis. Because multiple probes were used to measure gene expression for a gene, search returns are reported by probe rather than by gene. The microarray data         is presented in a "heat map" format where the colors of the heat map correspond either to raw         data or to a normalized (z-score) expression level of a probe. Brain structures are organized such         that moving left to right on the x-axis is analogous to moving from anterior to posterior first in         the cortical areas, followed by subcortical areas, cerebellum and brainstem.


!visualizing.jpg|border=1!

h4. Data Aggregation and Normalization

Unless viewing data on the lowest possible resolution, the heat maps presented on this site are based on data aggregated within       brain structures. That is, when there are multiple samples for a given       structure, the value represented in the heat map will be the average of those sample values.

We further aggregate the expression values up the ontology tree, eg. Frontal Lobe will have a single averaged expression value, which is the average value 	  for all samples belonging to the Frontal Lobe.

Data represented in the heat maps has been normalized across the entire data set 	  before it is aggregated, and is normalized again for each probe when the heat map is constructed.

h3. Heat Maps

The "heat map" is a visualization of the microarray values for the returned probes of interest. 	  Each row of the heat map represents a probe. 	  Each column of the heat map either represents a tissue sample or anatomical brain structure 	  depending on the selected Resolution (Coarse, Structures, or Sample). 	  The colors of the heat map are normalized expression values. 	  Default heat map colors are in the green -- red scale where the color green 	  should be interpreted as relatively low expression and red as relatively high expression within the scope of each       probe.

The color scheme used for the heat map display can be changed to suit the user. You can use the       color map bar at the bottom of the heat map to display different normalized (z-score) color representations       of the heat map data (i.e. blue-red vs. green-red)or you can visualize log2 normalized expression map where the color       scale ranges from dark blue, representing low expression, and passes through cyan, yellow, orange and finally to dark       red, representing high expression.

Clicking on a cell of the heat map will bring up detailed information in the area above the heat       map. In the panel on the left, information about the sampled anatomical structure is displayed.       The stack of structures represents the hierarchy from the structure ontology. For more details on       the ontology see [Ontology and Nomenclature|^Ontology.pdf], or       the Help section on the ontology viewer [here|#Ontology Browser].

Additional information is shown in the middle panel, and includes gene symbol, gene name, probe name,        the log2 expression value and z-score and links to related data in other Allen Brain Atlas resources.        Links to donor meta-data are also included in this panel. Blue text indicates a hyperlink,        where there is more information available by clicking on the text.
The "Brain Explorer" link, when selected for the first time, will take you to a page where you         can download the Brain Explorer® 2 3-D viewer software. Once the  Brain Explorer program is loaded, clicking on the "Brain Explorer" icon will launch a desktop software application for viewing         the Atlas gene expression data in three dimensions.


!more_info.jpg|border=1!


The "Planar View" icon launches the [multiplanar viewer|#Multiplanar Viewer] that shows the expression         profile for the selected probe in the context of the donor brain.

The columns of the heat map have a different meanings depending on the selected resolution.         There are three resolution options available from the drop-down menu under the heat map: Coarse,         Structures and Samples. If "Samples" is selected there is a one-to-one correspondence         between a column and a physical tissue sample. In the Atlas, there are         typically multiple samples for each structure of interest. This oversampling may provide         information on variability and spatial gradients. In "Structures" mode, all samples         belonging to the same designated structure are combined and averaged together. In "Coarse"         mode, the brain is divided into approximately 20 large neuroanatomic divisions or regions (e.g.         frontal lobe, occipital lobe, striatum, dorsal thalamus, ventral thalamus). Samples within         each partition are averaged together to provide a summary value for the partition.

Data from multiple brains may be viewed in two ways. By default, columns are grouped first by         donors then by structures, allowing a user to compare the full expression profiles of the individual         brains side-by-side. Grouping the columns initially by structures then by donors allows a user to         view the data for each brain structure with data form all donors grouped side-by-side under that structure. You can toggle         between the two groupings by clicking the toggle button over the scroll bar.

h4. Comparing Genes of Interest


!compare_genesHBAPdyn.jpgpng|border=1!



You can add probes of interest to a collection for later viewing. 	  Check the checkbox at the left end of a search result row to add it to your collection. 	  Your choices are stored in a browser 'cookie' on your computer and will remain in effect 	  until you click the "Clear Selections" button, or clear your web browser's cookie cache.

Click the "View Selection SelectionsHeatmap" button to see all of your selections.

Please noteas thata thisheat featuremap. requiresAlternatively thatchoose you“View haveSelection cookiesThumbnails” enabledto inview your browser,selection 	as 3-D which is already the case for the rotating thumbnails.


!spinningcart.png|border=1!



In “Thumbnails” mode each row represents a probe with data from each donor arranged from left to right. The color patches in the thumbnail represents a physical tissue sample using the same user specified color scheme as for heatmap viewing. Clicking on a patch will turn it bright blue and bring up detailed information in the area above the thumbnails. To rotate the thumbnail, drag the black downward triangle on the slider labeled “Rotate”. You can switch between viewing left cortical, right cortical and sub cortical samples using the “Left Cortex”, “Right Cortext” and “Subcortex” buttons located above the thumbnails. Cortical samples projected on a standard inflated white matter surface while sub-cortical samples are displayed as spheres in their 3D sampling locations.

Please note that this feature requires that you have cookies enabled in your browser, 	  which is already the case for the great majority of users.




h3. Gene Detail

Under Gene Info, clicking on the Gene Symbol or Gene Name of your Search results will take you to a microarray gene detail page.

The microarray gene detail page displays information about the gene including  	  Organism, Chromosome, Entrez Gene ID, related data from other Allen Brain Atlas resources,  	  Gene Name and Alternate Symbols.  	  Detailed expression heat maps for each probe are stacked by donor for a direct comparison between brains.  	  There is also a section of links to external resources.




h3. Probe Detail

Clicking on the Probe Name will take you to the microarray probe detail page.

The microarray probe detail page displays information about the probe including  	  probe ID, Gene Symbol, Gene Name, Probe Name, NCBI Accession and GI numbers.  	  It also includes the probe type, length, GC percent and sequence information.  	  Detailed expression heat maps from each donor brain are stacked so as to directly compare the probe between brains. 	  There is also a section of links to external resources.




h3. Multiplanar Viewer

The Planar View link opens a multiplanar viewer that  shows sampling sites for microarray data 	  and indicates gene expression levels for a single probe 	  in coronal, sagittal and horizontal sections of MRI space for a given specimen. 	  Additional viewing frames show spatially correspondent histological data 	  at the slab and block levels with anatomic annotations 	  and specific delineations of sampling sites for microarray data generation.

h4. Multiplanar Navigation

In this image you see the multiplanar navigation controls. 	  Points from which microarray tissues samples were taken are colored 	  to show expression level, according to the active color map.


!multi_planar_view.jpg|border=1!

Click or click-and-drag to move the crosshairs on any of the three MRI views ports.

The various control and feedback components are labeled here 1 - 7:
# *Donor*: Identification number of the donor currently displayed in the viewer.
# *Probe Name*:  The label for the probe currently displayed in the viewer.
# *Brain Explorer Link & Permalink*: Click the Brain Explorer link view this gene in the Brain Explorer 3D viewer. Click the permalink component to generate a URL 	      that will bring you back to this page with the current location settings.
# *Scale, MNI Coordinates & Contrast*: Scale bar, MNI coordinates at the crosshairs. Click and drag to move the contrast control.
# *Brain Structure*:  This field is updated to indicate the structure under         the crosshairs.  Click on the structure label to launch the ontology browser in a new window.
# *Expression Level*: This component reports both the raw expression value         and its z-score-normalized value.
# *Color Map Window & Level*: adjust the upper & lower bounds, or slide the entire control         to modify the range of colors used to map expression levels.

h4. Image and Probe Navigation


!MP_image_viewers.jpg|border=1!

In this image you see the heat map associated with a single, user-defined probe of interest as well as two image viewers illustrating the 2D histology associated with the point selected     by the MRI crosshairs.  The viewer     on the left-hand shows a larger view of the relevant brain slab, with a blue highlight     around the block of that slab from which the selected sample was taken.  The     viewer on the right-hand side shows a detailed view of that block, with structure annotations visible.

You can navigate from the image viewers as well. The strip of thumbnail images     at the bottom of each viewer shows all of the images from its parent specimen, in sectioning order.     Clicking on a thumbnail image in the left-hand viewer will move the MRI crosshairs     and open a new set of images in the right-hand viewer.  Click on one of the structures to move     the MRI crosshairs to the location where that structure was sampled.       As you move your mouse over the structures in the right-hand viewer its name       will appear in the upper-left corner of the viewer.

The toolbar icons provide more detailed views of the tissue sections:

| !outline.png|border=1! | Add or remove annotated structure outline |
| !structureColors.png|border=1! | Add or remove annotated structure colors |
| !structureLabels.png|border=1! | Add or remove annotated structure labels |
| !Allspecimen.png|border=1! | Show all sections from this specimen |
| !blockface.png|border=1! | Show block-face images |
| !showInSIV.png|border=1! | Launch Single Image Viewer in another window |


h3. Ontology Browser

Click on a Structure acronym link in either the microarray search returns page or the Planar View page    to open a new window with the Ontology Browser for the Allen Human Brain Atlas.

The expandable tree view of the anatomic structures is color coded and serves as a     legend to the anatomic structures on other pages in the Atlas.