ALLEN Human Brain Atlas

This is the online help for the Human Brain Atlas web application.

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The Data Set

The Allen Human Brain Atlas consists of two primary sources of gene expression data: microarray numerical value data and in situ hybridization (ISH) image data.

For complete details please see the Microarray Platform Selection, Whole Brain Microarray and In SituHybridization white papers on our Documentation page.

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Supported Platforms

This application has been tested with the following configurations. You may notice irregularities with software that has not been tested. There are known issues when viewing heat map data using unsupported browsers.

Before you install/upgrade Flash Player, uninstall existing players using the Adobe uninstall program.
There are uninstallers available for Windows or Macintosh.

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Microarray Data

The Data Set

The website offers three types of searches to allow a user to: (1) limit the visualization to a subset of probes (or genes) of interest (Gene Search); (2) use a 'seed' gene to find other genes with similar expression patterns (Find Correlates); and (3) compare expression between different anatomic regions (Differential Search).

Gene Search

To search for a gene category by disease, pathway, cell type or function, click on the relevant search term in the tag cloud. 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 or Entrez Gene ID in the search box (multiple genes searches require an OR between gene names) before clicking the Search button.

Boolean Syntax

The following special operators can be used to build queries:

• 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 (&).
• Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
• The NOT operator (!)is not supported within parenthesis.

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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 and Allen Developing Mouse Brain Atlas and the NIMH Transcriptional Atlas of Human Brain Development.
To find other genes with 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. 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.

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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 a higher expression in one structure when compared to another structure, enter the target brain structure in the top search box and your contrast region in the bottom search box and click on the Search button.
Your search will return results in the two brain regions selected. The results will show higher expression in the target region compared to the contrast region. (To view the expression patterns of the returned probes over 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.
To perform the previous search in reverse, click the toggle button beside the Search button.

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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. 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.

Data Aggregation and Normalization

Unless viewing data from a single sample, the heat maps presented on this site are based on data aggregated within brain structures ("Averaged Samples", see below). 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, i.e. 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.

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, Averaged Samples, 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 map 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, or the Help section on the ontology viewer here.

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 Institute projects. 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 Brain Explorer® 2. Once Brain Explorer 2 is loaded, clicking on the Brain Explorer link will launch a desktop software application for viewing the Atlas gene expression data in three dimensions.

The "Planar View" link launches the 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 meaning depending on the selected Resolution. There are three options available from the drop-down menu under the heat map: Coarse, Averaged Samples 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 "Averaged Samples" 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, etc.). 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 expression profile of the individual brains side-by-side. Grouping the columns initially by structures then by donors allows a user to mix the data of the brains in the dataset within a combined brain structure profile. You can toggle between the two groupings by clicking the toggle button over the scroll bar.

Comparing Genes of Interest

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 Selections' button to see all of your selections.

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.#Return to top

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Gene Detail

Clicking on the Gene Name or Gene Symbol of your Search results will take you to the 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.

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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.

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Brain Explorer 2 Application

Brain Explorer 2 is a desktop software application for viewing human neuroanatomy and the Allen Human Brain Atlas microarray gene expression data in the framework of the Magnetic Resonance Images of the sampled brains.

Once you have chosen a gene of interest (by clicking on the heat map), you can explore a three dimensional representation of its gene expression by clicking on the "Brain Explorer" link over the heat map. When Brain Explorer opens, you will be taken to a screen that displays the Image Viewer, the Structure Ontology Viewer, and the Gene List.

Image Viewer

The Image Viewer will automatically show the 3D expression representations of your gene of interest on every sampled brain. Cortical gene expression is overlaid on an inflated white matter surface for each donor brain, with spots under the white surface representing gene expression in the subcortical regions of the brain. A striped expression pattern on the cortical surface is a result of having sampled from every other slab of cortical tissue. Under each representative brain is the heat map for the probe you selected. Clicking on that heat map will pinpoint the area in the brain from which the sample was taken.

The gene expression colors correspond to the settings in the Atlas with which you were viewing the original heat map. To change the gene expression representation, click on the "Gene" tab in the top left hand corner of your screen and choose either z-score or raw data representations of the gene expression data.

A compass in the right hand corner of the image viewer depicted by a stylized head can be used to rotate the brains by clicking and dragging your cursor. You can look at a single brain by clicking on the magnifying glass above that brain. Choosing a data point, either by clicking on the heat map below the brain or on a brain region itself, will bring up the gene symbol, the location of the sample and the expression level and z-score in the left hand corner of the Image Viewer.

You can zoom using either the wheel on your mouse or using the Zoom scrollbar in the lower right hand corner of the Image Viewer.

Structure Ontology Viewer

The Structure Ontology Viewer shows the entire collapsible ontology for the human brain including the color coding used by our expert annotation team to visualize structural boundaries. Two columns to the right of the ontology determine the type of data displayed in the Image Viewer. "A" represents annotation and when checked, will show a visual representation of that structure in the Image Viewer. "G" represents gene expression and when checked, will show gene expression in that structural domain.

The default organization for the Structure Ontology is the Hierarchical View, but if you are unfamiliar with the ontology, you can click on the Alphabetical View to see the structure list in alphabetical order.

The Bookmarks tab is a space where you can create and save favorite views of the brain. Several default views are already saved that will rotate the brain back into common viewing frames.

Gene List

This section displays the gene probes you have selected and downloaded in this session. When more than one gene probe has been downloaded, clicking on one probe will show its gene expression profile in the image viewer. Right clicking on the gene probe name will bring up a menu where you can view the gene detail page (Get Info), be taken to the Multiplanar View of the probe (View Images) or copy the gene information for use in another application.

Toolbar

Advanced Features

Atlas Tab:

You can show opaque three dimensional structures of the brain by "showing" or "hiding" structures from this menu. The "Transparent" function allows you to see transparent views of the structures to view the anatomical relationships between them.

Selecting the sagittal, coronal or horizontal sections (or clicking on one of the section image buttons in the toolbar) will superimpose a single plane of the MRI images from each brain on your image space. These planes can be moved once the selection tool mode button in the toolbar is selected. Selecting "Show Annotation on Section" from this menu will color the MRI images according to the brain structure ontology.

Gene Tab:

When you have a gene selected, the Gene Tab menu allows to you to show all expression, hide all expression (for instance to then select a single structure) or toggle expression (for instance, unselect your region of interest then toggle to see expression in only that region).

You can also show or remove threshold controls and choose the visual representation of your data (raw data vs. z-score) from this menu.

To be taken to the gene detail page, select "Get Info". To see the Multiplanar view, choose "View Images". These functions are also available by right-clicking on the gene name in the Gene List.

Clipping Planes:

When this function is selected, either by toggling the cutting tools button in the toolbar or selecting "Clipping Planes" from the View drop down menu, you can make coronal, sagittal or horizontal cuts in your view of the brain and related data. To cut in a particular plane, make sure the cursor is in selection tool mode, and then click and drag on the plane you are interested in clipping.

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Multiplanar Viewer

The Multiplanar Viewer 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 level with anatomic annotations and specific delineations of sampling sites for microarray data generation.

Multiplanar Navigation

In the image to right 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.

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:

1. Donor: Identifier of the donor currently displayed in the viewer.
2. Probe Name: The label for the probe currently displayed in the viewer.
3. Permalink: Click the permalink component to generate a URL that will bring you back to this page with the current location settings.
4. Contrast: Click and drag to move the contrast control.
5. 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.
6. Expression Level: This component reports both the raw expression value and its z-score-normalized value.
7. 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.

Image and Probe Navigation

In the image at left you see the 2D images associated with the point selected by the MRI crosshairs. The viewer on the left hand shows a larger view of the brain specimen, with a blue highlight around the chunk of that specimen from which the current sample was taken. The viewer on the right hand shows a detailed view of that chunk, 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.

Use the toolbar icons to add or remove structure annotations such as structure outline, structure colors, and structure labels. To show all specimen images from this block in order, including the Nissl, ISH, SMI-32 and pre- and post-cut LCM images, click . To see the block face images, click . Use the full-page viewer icon to launch a new full-page viewer in a new window for the current image set.

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Microarray Specimen Magnetic Resonance Images (MRI)

Select the MRI tab to view the Microarray Specimen MRI page, or click on a Donor link in the Gene Detail or Probe Detail pages.

The Microarray Specimen MRI page displays axial, coronal and sagittal planar MRI images of the brain. Drag the red axes in order to change the view coordinates. Donor information including Organism, Age, Sex, Ethnicity, and Postmortem Interval (PMI).

The MRI data files are available for download in NIFTI format by clicking on the T1, T2 and DTI links.

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Raw Microarray Data Download

To download the raw microarray data for tissue samples in the Allen Human Brain Atlas, click on the Download tab.

Searching by Structure

With the Search by Structure Name radio button selected, type in the text box to see some search suggestions from the Allen Human Brain Atlas brain structure ontology. Check the Include Descendents check box to include structures below the selected structure in the structure ontology. Select from the list of suggestions, or just click the Search button to search for your structures. For more details on the ontology see Ontology and Nomenclature, also the Help section on the Ontology Browser.

For each tissue sample, the Microarray Data Download page has an entry listing the Tissue Sample ID, the Structure name, the RNA Integrity Number, the Experiment number, the Array number, the sample Type, the RNA in Labeling Reaction, the RNA in Array and a link to the raw microarray data file for the tissue sample in Agilent Feature Extraction output file format.

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Ontology Browser

Click on a Structure acronym link in the Microarray Search page or the Microarray Multiplanar View to open a new window with the Ontology Browser for the Allen Human Brain Atlas.

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

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In Situ Hybridization (ISH) Data

Gene expression data is available as colorimetric in situ hybridization (ISH) for specific brain regions. Images are grouped into image series that comprise an experiment. Experiments consist of slides from the same specimen that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular gene.

The projects include 1,000 Gene Survey in Cortex (Cortex Study), Schizophrenia Study, and Subcortex study. Please refer to the In Situ Hybridization white paper in the ALLEN Human Brain Atlas Documentation tab for the details.

Choose among the following options for retrieving the data:

• Search by Gene Category (from the tag cloud)
• Gene Search
• Search by Study

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ISH Gene Search

Gene Search

You can search for experiments associated with a gene using its gene symbol, name, Homologene Group ID, or Entrez Gene ID. First, select the "Gene" radio button, type the search term in the input box and click the "Search" button. You will be offered suggestions to choose from while you type, but you can also search by typing the first three or more letters in its name or symbol and appending an asterisk ( * ) as a wildcard.

Search by Study

Data includes ISH experiments from three separate projects including: 1,000 Gene Survey in Cortex (Cortex Study), Schizophrenia Study, and Subcortex study. Please refer to the In Situ Hybridization white paper in the ALLEN Human Brain Atlas and the gene list for details.

You can restrict your search to a single study and search for experiments associated with a gene from that study.

First, select the relevant radio button: Subcortex Study, Cortex Study or Schizophrenia Study. You will then have a choice to limit your search based on additional criteria such as sex of the donor, hemisphere, etc., depending on the study. Then type the search term in the input box and click the "Search" button. To see a list of genes surveyed in that study, please look at the gene list in the documentation tab. Clicking the "Search" button without any entry in the input box will return a list of genes and the accompanying data for that study.

The following search criteria can be specified in the text box to the right of the categories. If you copy + paste in a list of terms delimited by tabs or carriage returns they will automatically be converted into a list of search criteria separated by the OR operator ( | ).

Boolean Syntax

The following special operators can be used to build queries:

• 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 (&).
• Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
• The NOT operator (!)is not supported within parenthesis.

Search Results

Click a column heading to sort the search results. Click it again to toggle ascending to descending order. ISH search results include the following columns:

Select an image series by clicking the checkbox in the first column, then click the "View Selected Experiments" button to view all of your selections' images. Click "Clear Selection" to deselect all of your selections, or click "View Cart" to manage them.

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Viewing Images

Zoom and Pan (ZAP) Image Viewer

The ZAP Image Viewer allows you to navigate through an image series' thumbnails to select an image to view at higher resolution. Once selected, you can manipulate it with your mouse and use the keyboard or toolbar to take additional actions.

Choose a different viewer size by selecting it from the dropdown menu above the viewer(s). If you are viewing more than one image series, choose a different table layout by selecting a different number of columns. Drag viewers to other cells in the table to rearrange them.

Multiple image series can be opened on the same Web page to enable side-by-side comparisons. You can swap viewers' locations on the page by clicking on the first viewer's title bar and dragging it to the second viewer's location.

The gene symbol or treatment type is displayed in the title bar along with the Allen Institute image series ID. Additional details are displayed across the top of the viewing area, including the image index, tissue index, and tissue location.

Thumbnails for the entire image series are displayed across the bottom of the viewer in section order. Click a thumbnail to select it for viewing, or use the keyboard to navigate through the set. The current selection is outlined in black.

Side by Side Nissl Viewing

Once you click on the full screen viewer button, you will be taken to a screen with side by side viewers. The left hand viewer shows the ISH image series and the right hand viewer displays the Nissl image series from the same specimen block. To show the nearest Nissl section to the ISH image you are interested in, click the "Sync" checkbox. Clicking on another ISH image will automatically display its nearest Nissl section. Clicking on an image thumbnail in the Nissl image series will automatically take you to the nearest ISH image. While the "Sync" box is checked the Pan and Zoom functions will affect both ISH and Nissl images.

Scale Bar

Shows the current viewing resolution of the image, in microns. This value dynamically changes as you zoom in/out of the image. You can position the scale bar anywhere on the main image by dragging the scale bar by its ruler.

You can toggle the orientation of the scale bar from horizontal to vertical by clicking on the scale bar text.

Toolbar

Keyboard Commands

Expression Mask Colors

The Expression Mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).

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Specimen Detail Information

Specimen Block Layout

Specimens are received as variable sized blocks of frozen tissue. Before they are sectioned for ISH experiments they are divided into a number of sub-specimens. Throughout this site, when we refer to a specimen we are actually referring to one of these sub-specimens.

The specimen block layout diagram is intended to put the current sub-specimen in context of its original tissue block, and to help navigate to nearby sub-specimens.

In the block diagram, the green block represents the current sub-specimen. Sibling sub-specimens are shown as grey blocks. Clicking on one of the siblings updates the current page to show the sibling's information.

Donor/Specimen Metadata

pH - tissue sample pH
RNA Integrity Number - metric indicating RNA integrity from tissue. Ranges from 1 to 10 (degraded to intact RNA)
Postmortem Interval - hours between time of death and time tissue samples frozen
Hemisphere - right or left hemisphere tissue origination
Tissue Location - tissue origination in brain
Specimen ID - internal ID
Sex - male or female
Race - ethnicity
Age - years
Handedness - right, left, or ambidextrous
Disease Categories - control or schizophrenia
Smoker - yes or no
Donor ID - internal ID

Sectioning Diagram

The sectioning diagram attempts to depict the relationship between the sections taken from a specimen, the position of each section, and the genes for which experiments have been run on those sections.

Each section consists of 100% of the specimen in the plane of sectioning. The section number, or "section index" is an indicator of relative depth into the specimen.

To the left of the section diagram is a preview image. As you move your mouse pointer over the section diagram squares, the preview will be updated to show the corresponding image. You can get a larger view of the preview image by clicking your mouse on the section squares to launch an image viewer on a separate page.

Each of the colored squares at the top of the diagram represents one section. By default, the sections are ordered by section index. The different colors are mapped to the different genes tested against each section. The color-to-gene mappings can be found in the rectangular gene symbol map appearing below the set of sections.

Each rectangle in the gene symbol map has the same color as one or more of the section squares, and represents either the genes targeted for ISH, or the particular stain applied to the corresponding section blocks.

Hovering the mouse pointer over the rectangles will highlight the associated section squares for easy identification. Each rectangle is labeled with either a gene symbol or a stain treatment abbreviation.

You can click your mouse on the rectangles to go to an Image Summary page, where you can get more information about the section images generated from a particular treatment, and get summary information about gene probes.

Diagram tools

On the right of the titlebar of the Sectioning Diagram, you will find two diagram display tools, which are described below.

Contrast Slider

Drag this slider to the left or right to adjust the contrast of the preview image. Dragging the slider to the left makes the image lighter, dragging the slider to the right makes the image darker.

Section Ordering

Click this button to sort the section diagram by gene rather than section index. Click it again to return to the default ordering.

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Gene Detail Information

This page summarizes the data regarding the selected gene. The main section details its full name, entrez gene id, alternate gene symbols, chromosome, organism, links to related data in other projects, and gene categories that have been applied to it. A link below this section allows you to bring up a summary of all of the experiments (image series) for this gene.

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Image Series Information

The image series details include the gene and probe associated with the experiment, as well as information regarding the specimen.

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