There are two sets of microarray data in this resource; Micro- and macrodissection studies, both assayed on the Affymetrix GeneChip Rhesus Macaque Genome Arrays. The Macrodissection study includes microarray data assayed from samples that were dissected manually from four postnatal stages in five specific sample tissue locations; medial frontal cortex (areas 24, 25 and 32), occipital cortex, hippocampal cortex (hippocampal formation), amygdaloid complex and basal nuclei (basal ganglia). The Microdissection study looks at smaller more targeted subdivisions of the structures considered in the macro study in four postnatal stages and six prenatal stages. These smaller regions, such as a single cortical layer of cells, were microdissected using a laser dissection microscope. To choose between these data sets, select “Microdissection” or “Macrodissection” from the Microarray drop down menu.
MICRODISSECTION MICROARRAY
Searching
You can browse the data using the three search tools: (1) Gene Search, to obtain gene expression data for specific genes of interest, (2) Differential Search, to compare expression between two sets of brain structures at desired developmental stages, and (3) Correlative Search, to find genes that have an expression pattern similar to a “seed gene” selected from the results of a Gene or a Differential search.
Some search modes offer additional information, accessible by clicking on the “?” next to the Search button.
Gene Search
To search for probes associated with a specific gene, select the Gene Search radio button, type the gene name, gene symbol or Entrez Gene ID in the search box and click the “Search” button. You can also select an entry from the list displayed as soon as you start typing. To be able to search the Macaque database for human gene homologues, search using:
- gene symbol
- gene aliases
- gene name
- Entrez ID (NCBI)
- Ensembl ID
- Affymetrix Probeset ID
The search results are displayed in the form of a heat map showing the expression values for the probes that match the search criteria. Since the microarray may have more than one probe per gene, the heat map’s left panel shows Gene Symbol and Probe Name for each row.
Gene symbols and gene names are displayed as follows:
- If the probe targets a Macaque NCBI gene then the gene abbreviation will be displayed unaltered (eg. CLEC1A)
- If the probe targets a Human NCBI gene then the gene abbreviation will be displayed inside parentheses (eg. (CLEC1A))
- If the probe targets a Macque Ensembl gene then the gene abbreviation will be appended with the Ensembl ID in parentheses (eg. CLEC7A(ENSMMUG00000002192))
- If the probe targets a Macque Ensembl gene and there is no available gene name, then the Ensembl ID will be used as the gene name (eg. ENSMMUG00000018691)
See Microarray Data Visualization for information on reading heat maps.
Differential Search
This dataset can be searched to find genes that show enrichment of expression in one set of samples compared to another set of samples. Those samples can correspond to different brain structures and/or different developmental stages. To perform this type of query, select the “Differential Search” radio button. To find genes or probes with enhanced expression profiles in a target set of samples when compared to a contrast set of samples, first select the Target and Contrast Structures by starting to type the structure name in the text box - a structure ontology of the applicable structures will appear and you can select from this menu. Then, select the desired developmental stages using the Ages drop down boxes for both the Target and Contrast Domains.
You can reverse Target and Contrast Domains by pressing the toggle button above the Search button.
Search Results
The search results will shown in the form of a Heatmap with genes that exhibit higher expression in the target domain ranked higher than those in the contrast domain by either p-value or by fold change. To alter the sort parameter, click on either the “p-value” or the “Fold Change” buttons. Since the macaque genome is not fully annotated, many probes do not have a corresponding associated gene. In those cases, the probe name is displayed under the Gene Symbol label.
Correlative Search
Since genes with similar expression patterns may be related in function, the NHP Atlas includes functionality to search the dataset for genes whose expression over a given set of structures or developmental stages resemble the expression pattern of a gene of interest.
First, the gene of interest must be selected from the heatmap returned by a Gene or Differential search by clicking on a data-point in the heatmap. The corresponding probe will be displayed under the “Find Correlates” button close to the top right corner of the heatmap. Next, select the desired structures and developmental stages from the drop down menus and then click “Find Correlates”.
The resulting heatmap displays the list of probes based on the search criteria ranked by Pearson’s correlation “r” with the gene of interest. To find the anti-correlate, click the “r” button.
To filter the heatmap display to show specific structures or developmental stages, use the “Filter Heatmap” function at the bottom of the heat map.
Microarray Data Visualization
The results for all three types of searches against microarray data are displayed in two horizontal page sections:
- The bottom section contains the heat map representation of the data returned by the search operation.
- The top section contains probe, sample and expression information for the data point selected by clicking on a cell in the heat map.
Heatmap
Based on your search, the resulting microarray data are presented as a matrix with brain structure and developmental stage on the horizontal x-axis and gene probes on the vertical y-axis. On the horizontal axis, developmental stages are represented on top, color coded in shades of gray such that moving from left to right corresponds to increasing age. Brain structures are represented in bright colors immediately below, such that moving left to right corresponds to moving in the anterior to posterior direction, first in the cortical areas, followed by subcortical areas, cerebellum and brainstem.
Each column therefore represents a structure for a specific developmental stage. On the vertical axis, each row represents a probe rather than a gene, because multiple probes were used to measure gene expression for a gene. Additionally, since the macaque genome is not fully annotated, many probes do not have a corresponding associated gene. In those cases, the probe name is displayed under the Gene Symbol label.
The microarray data is presented in a heat map format where the colors of the heat map correspond either to normalized data (log2 Intensity) or to a normalized (z-score) expression level of a probe. Default heat map colors the z-score in the green – red scale, where green represents underexpression and red overexpression of that gene compared to expression throughout the brain. The window and level for the colors may be adjusted, and other color schemes may be selected, by using the Color Map control under the heat map. The slider on the bottom right can be used to adjust the zoom level. In the top right hand corner of the heat map, there is a toggle button, which when clicked will sort the heat map data either by donor or by structure.
To view expression patterns of the returned probes in specific regions of the brain or in specific developmental stages, filter the heatmap display from the function below the heat map.
You can select a set of probes for later use by checking the checkboxes besides the list of gene symbols. Your choices are stored in a browser ‘cookie’ in 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 Heatmap” button to see your selections.
Clicking on a heat map cell populates the top section of the page with detailed information about that cell. This information includes gene symbol, gene name, NCBI Entrez ID, probe name, chromosome, as well as the sample’s structure and specimen’s age. It also shows the exact expression values by their log2 intensity and z-score.
The section also contains buttons to navigate to related data in other Allen Brain Atlas resources.
Filter Heatmap
If you are interested in narrowing the number of donors or structures, use the “Filter Heatmap” function below the heatmap. Clicking on the “…” button will bring up a menu where you can choose the donors and structures you’d like to visualize. Once you have saved your options, turn on the Filter Heatmap function by clicking the button.
MACRODISSECTION MICROARRAY
This dataset includes microarray data manually dissected from five brain regions; medial frontal cortex (areas 24, 25 and 32), occipital cortex, hippocampal cortex (hippocampal formation), amygdaloid complex and the basal nuclei (basal ganglia), from four post-natal stages.
Searching
You can browse the data using the three search tools: (1) Gene Search, to obtain gene expression data for specific genes of interest, (2) Differential Search, to compare expression between two sets of brain structures at desired developmental stages, and (3) Correlative Search, to find genes that have an expression pattern similar to a “seed gene” selected from the results of a Gene or a Differential search.
Some search modes offer additional information, accessible by clicking on the “?” next to the Search button.
Gene Search
To search for probes associated with a specific gene, select the Gene Search radio button, type the gene name, gene symbol or Entrez Gene ID in the search box and click the “Search” button. You can also select an entry from the list displayed as soon as you start typing. To be able to search the Macaque database for human gene homologues, search using:
- gene symbol
- gene aliases
- gene name
- Entrez ID (NCBI)
- Ensembl ID
- Affymetrix Probeset ID
The search results are displayed in the form of a heat map showing the expression values for the probes that match the search criteria. Since the microarray may have more than one probe per gene, the heat map’s left panel shows Gene Symbol and Probe Name for each row.
Gene symbols and gene names are displayed as follows:
- If the probe targets a Macaque NCBI gene then the gene abbreviation will be displayed unaltered (eg. CLEC1A)
- If the probe targets a Human NCBI gene then the gene abbreviation will be displayed inside parentheses (eg. (CLEC1A))
- If the probe targets a Macque Ensembl gene then the gene abbreviation will be appended with the Ensembl ID in parentheses (eg. CLEC7A(ENSMMUG00000002192))
- If the probe targets a Macque Ensembl gene and there is no available gene name, then the Ensembl ID will be used as the gene name (eg. ENSMMUG00000018691)
See Microarray Data Visualization for information on reading heat maps.
Differential Search
This dataset can be searched to find genes that show enrichment of expression in one set of samples compared to another set of samples. Those samples can correspond to different brain structures and/or different developmental stages. To perform this type of query, select the “Differential Search” radio button. To find genes or probes with enhanced expression profiles in a target set of samples when compared to a contrast set of samples, first select the Target and Contrast Structures from the drop-down menu. Then, select the desired developmental stages using the Ages drop-down boxes for both the Target and Contrast Domains.
You can reverse Target and Contrast Domains by pressing the toggle button above the Search button.
Search Results
The search results will shown in the form of a Heatmap with genes that exhibit higher expression in the target domain ranked higher than those in the contrast domain by either p-value or by fold change. To alter the sort parameter, click on either the “p-value” or the “Fold Change” buttons. Since the macaque genome is not fully annotated, many probes do not have a corresponding associated gene. In those cases, the probe name is displayed under the Gene Symbol label.
Correlative Search
Since genes with similar expression patterns may be related in function, the NHP Atlas includes functionality to search the dataset for genes whose expression over a given set of structures or developmental stages resemble the expression pattern of a gene of interest.
First, the gene of interest must be selected from the heatmap returned by a Gene or Differential search by clicking on a data-point in the heatmap. The corresponding probe will be displayed under the “Find Correlates” button close to the top right corner of the heatmap. Next, select the desired structures and developmental stages from the drop down menus and then click “Find Correlates”.
The resulting heatmap displays the list of probes based on the search criteria ranked by Pearson’s correlation “r” with the gene of interest. To find the anti-correlate, click the “r” button.
To filter the heatmap display to show specific structures or developmental stages, use the “Filter Heatmap” function at the bottom of the heat map.
Microarray Data Visualization
The results for all three types of searches against microarray data are displayed in two horizontal page sections:
- The bottom section contains the heat map representation of the data returned by the search operation.
- The top section contains probe, sample and expression information for the data point selected by clicking on a cell in the heat map.
Heatmap
Based on your search, the resulting microarray data are presented as a matrix with brain structure and developmental stage on the horizontal x-axis and gene probes on the vertical y-axis. On the horizontal axis, developmental stages are represented on top, color coded in shades of gray such that moving from left to right corresponds to increasing age. Brain structures are represented in bright colors immediately below, such that moving left to right corresponds to moving in the anterior to posterior direction, first in the cortical areas, followed by subcortical areas, cerebellum and brainstem.
Each column therefore represents a structure for a specific developmental stage. On the vertical axis, each row represents a probe rather than a gene, because multiple probes were used to measure gene expression for a gene. Additionally, since the macaque genome is not fully annotated, many probes do not have a corresponding associated gene. In those cases, the probe name is displayed under the Gene Symbol label.
The microarray data is presented in a heat map format where the colors of the heat map correspond either to normalized data (log2 Intensity) or to a normalized (z-score) expression level of a probe. Default heat map colors the z-score in the green – red scale, where green represents underexpression and red overexpression of that gene compared to expression throughout the brain. The window and level for the colors may be adjusted, and other color schemes may be selected, by using the Color Map control under the heat map. The slider on the bottom right can be used to adjust the zoom level. In the top right hand corner of the heat map, there is a toggle button, which when clicked will sort the heat map data either by donor or by structure.
To view expression patterns of the returned probes in specific regions of the brain or in specific developmental stages, filter the heatmap display from the function below the heat map.
You can select a set of probes for later use by checking the checkboxes besides the list of gene symbols. Your choices are stored in a browser ‘cookie’ in 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 Heatmap” button to see your selections.
Clicking on a heat map cell populates the top section of the page with detailed information about that cell. This information includes gene symbol, gene name, NCBI Entrez ID, probe name, chromosome, as well as the sample’s structure and specimen’s age. It also shows the exact expression values by their log2 intensity and z-score.
The section also contains buttons to navigate to related data in other Allen Brain Atlas resources.
Filter Heatmap
If you are interested in narrowing the number of donors or structures, use the “Filter Heatmap” function below the heatmap. Clicking on the “…” button will bring up a menu where you can choose the donors and structures you’d like to visualize. Once you have saved your options, turn on the Filter Heatmap function by clicking the button.
