Contents
Supported Platforms
This application has been tested with the following configurations. You may notice irregularities with software that has not been tested.
Microsoft Windows XP sp2, Vista
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Apple Macintosh OSX 10.3.6, 10.4
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Searching
There are two ways to search the data on the "Human Cortex Study " site; "Gene Search" and "Advanced Search."
Gene Search
"Gene Search" appears on our Home page. A gene search will show you a list of all the experiments we've done involving a gene that matches your search criteria. A "Match" in gene search means that the text you type in is contained somewhere in the name, symbol or alternate symbol of the gene involved in the experiment.As you begin typing in the gene search box, a list of suggestions will appear. You can use your arrow keys or the mouse to move down, highlighting the desired entry. If you're using your mouse, click on the desired entry to select it, then hit your "Enter" key or click the Search button to perform the search. If you're using arrow keys, just hit "Enter" and the search will be run. If you don't want to use one of the suggestions, hit your "Esc" key or click your mouse outside the list and the it will disappear.
Advanced Search
The Advanced Search page has many more options. You can:- Use the check boxes to limit a gene search to any combination of gene name, symbol or alternate symbols.
- Search by NCBI EntrezGene ID, or by our internal Image Series ID or Donor ID.
- Search by Tissue location
- Search by specimen meta data, such as tissue pH, RNA integrity number or post-mortem interval .
- Search by donor age or sex.
Type-ahead suggestions will appear for the gene search and all of the ID entry fields. After selecting a suggestion, click the Search button or hit the Enter key to perform your search. As noted above, you can dismiss the list of suggestions by hitting the "Esc" key.
Search Results
The result set shows a collection of gene expression experiments.Please note-- If you searched by gene, it may appear that some of the rows do not match your gene criteria. Keep in mind that by default all of the alternate gene symbols (which are not shown in the result list) are included in a gene search. To see the alternate symbols for a gene, click on the gene symbol in the result list. If you want to exclude alternate symbols from your gene search, try the Advanced Search page.
Sorting
The results are initially sorted by
Gene Symbol in ascending order. Click on any of the column headers to sort by that column; click on the
same column header again to reverse the sort order. A small arrow will appear next to the currently sorted
column, indicating the sort order, as shown in the image at right.
Getting more detailed information
The Gene Symbol, Image Count, Specimen and Image Series items all link to more detailed information.Comparing Result Sets
In addition to the links found
in each experiment row, you can select multiple rows to compare side-by-side. Click the check box at
the far left of the desired rows, then click the "Compare Selected Experiments" button. Use the check box
in the column header to toggle all of the row check boxes on or off.
XML
As shown in the image above, at the bottom of the table there is a link to an XML document containing all of the data in the result set.
Gene Detail
Gene Symbol
This section shows some gene metadata. If there is a homologue for the current gene in the Mouse, a "Homologes from the Allen Brain Atlas" link will be included in this section. Clicking the link will open the corresponding Allen Brain Atlas summary page for the homologous mouse gene in a new browser window.Example Images
Up to four example images from the image series will be shown here. The example images are chosen as every nth image from the series, where n = (the total number of images in the series)/4.
Click on an example image to launch a high-resolution viewer. Each image clicked on will launch a new high-res viewer to facilitate side-by-side comparisons.
Experiment Info
This shows a brief summary of the experimental parameters. Click on the links in this secton to get more detail.
Image Controls
See details on the image toolbar here.External Resources
The External Resources section contains links to other organizations that provide gene expression data. These links open in a new browser window, and should show information related to the current gene.
Image Series Detail
Example Images
Up to four example images from the image series will be shown here. The example images are chosen as every nth image from the series, where n = (the total number of images in the series)/4.
Click on an example image to launch a high-resolution viewer. Each image clicked on will launch a new high-res viewer to facilitate side-by-side comparisons.
Image Controls
See details on the image toolbar here.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
refering to one of these sub-specimens.
The specimen block layout diagram (left) 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 will open a detail page for that specimen.
Donor/Specimen metadata
pH - Cerebellar tissue pH of each sample, where tissue pH may be an indicator of tissue and RNA quality.
RNA Integrity Number - A metric commonly used to indicate integrity of RNA extracted from tissue. Ranges from 1 to 10 to indicate degraded to intact RNA, respectively.
Postmortem Interval - Duration of time, in hours, between actual or estimated time of death and time that tissue samples are frozen.
Tissue location
Visual Cortex - Primary and secondary visual cortex dissected from medial occipital cortex around the calcarine fissure.
Temporal Cortex - Dissected from regions at approximately the level of the midbody of the hippocampus; comprises Brodmann's areas 21, 22 and in some cases 20.
External Resources
The External Resources section contains links to other organizations that provide gene expression data. These links open in a new browser window, and should show information related to the current gene.
Image Thumbnails
Click on any image to launch a high resolution viewer.
Image Controls
See details on the image toolbar here.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
refering to one of these sub-specimens.
The specimen block layout diagram (left) 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 will open a detail page for that specimen.
Donor/Specimen metadata
pH - Cerebellar tissue pH of each sample, where tissue pH may be an indicator of tissue and RNA quality.
RNA Integrity Number - A metric commonly used to indicate integrity of RNA extracted from tissue. Ranges from 1 to 10 to indicate degraded to intact RNA, respectively.
Postmortem Interval - Duration of time, in hours, between actual or estimated time of death and time that tissue samples are frozen.
Specimen Detail
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
experiemnts have been run on those sections.
Each section consists of 100% of the specimen in the plane of sectioning. Sections are 20 microns thick. In this diagram, each section is numbered with its "section index" which is its depth (in microns) into the specimen / 20.
Each of the colored squares in 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 gene symbol map appears just below the set of sections.
To the left of the section diagram is a preview image. As you move your mouse pointer over the section diagram the preview will be updated to show the corresponding image.
Diagram tools
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.
At right is an example of the section diagram ordered by gene.
Gene expression
This button toggles the correlation of gene expression to section diagram size.
The image at right shows an example of what the section diagram might look like with gene
expression toggled on.
Please NOTE: We are in the early stages of this project and the methods for determining and analysis of expression are subject to change. What's presented here is intended to be a guide to the relative expression within the context of the given specimen.
Currently, the expression value is determined by finding the ratio of
(area of expression)/(area of grey matter). That value is then scaled (currently by a factor of 10)
and clipped at 100 for display. When expression is toggled on, a section with a scaled
value of 100 shows as fully colored; a scaled expression value of 0 shows as completely white.
In cases where we were not able to determine an expression value, a white box with a question mark
"?" is shown.
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
refering to one of these sub-specimens.
The specimen block layout diagram (left) 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 will open a detail page for that specimen.
Donor/Specimen metadata
pH - Cerebellar tissue pH of each sample, where tissue pH may be an indicator of tissue and RNA quality.
RNA Integrity Number - A metric commonly used to indicate integrity of RNA extracted from tissue. Ranges from 1 to 10 to indicate degraded to intact RNA, respectively.
Postmortem Interval - Duration of time, in hours, between actual or estimated time of death and time that tissue samples are frozen.
Image Controls
The image toolbar contains buttons that allow you to flip between the ISH, expression mask & nearest Nissl images associated with each experiment.
Clicking on the image type buttons will switch the images to the selected type, as show below:
The toolbar also has a contrast control that
works with any of the image types. The contrast slider control is shown in use
with an expression mask image to the left.
To the right of the "Clossest Nissl" toolbar button is the "Reset" button. Click this to return to the default image type with no added contrast.