>
> |
Atlasing Use Cases from Maryann's AtlasIntegration Scenarios document (above)
USE CASE 1:
A researcher selects a region in the Smart Atlas and wants to know: “What genes are expressed in this location and what cells express each?” The first source to be consulted would be microarrays because they would have the largest numbers of possible candidates. However, depending upon the location covered by the microarray, it may not have the spatial resolution required to be certain that it is only targeting the desired location. The results from the microarray can be compared against in situ hybridization tissues to find out what mRNAs and DNA’s are found in this area and the cells that express them. Non-radioactive in situ hybridization has better spatial resolution but isn’t as sensitive as radioactive in situ hybridization. Depending upon the additional information that may be present in a section, e.g., Nissl stain, other counterstains, we may or may not be able to determine the cellular identity of labeled cells. We would then compare the list of genes against the proteins found in the area. Protein maps may yield additional candidates although just because a protein is found there, doesn’t mean that the gene is found there. Comparison of results with a connectivity map might resolve some of the discrepancies. A similar caveat applies to the GCSF: one would have to determine whether the signal is found in cell bodies, dendrites or axon terminals to determine whether or not we would expect the signal to be consistent with the microarray data.
Variations on the above query include: “What genes are expressed at high levels in location X and Y?” What genes are expressed in high levels in location X and low levels in location Y?”
USE CASE 2:
A researcher interested in the Parkinson’s disease model uses the Smart Atlas to investigate patterns of gene expression for genes determined through GeneNetwork to be affected in Parkinson’s disease. These patterns are used to focus investigations of anatomical alterations in the MRM or whole brain histology data available through the LONI or Neuroterrain atlases or retrieved through the Mouse BIRN data federation. Alternatively, changes observed from the MRM data can be used to issue a query in the Smart Atlas for gene expression patterns (or protein expression patterns) that correlate with the observed changes.
Additional Atlasing Use Cases
USE CASE 3:
A researcher is looking at the MDA atlas in MBAT and wishes to look at another atlas for additional information about cell structure in the dentate gyrus. They submit a ROI query in MBAT and pull up the corresponding region in the NT atlas (with the ROI outlined?). Then they would like to see if there are additional sub-divisions of this area, so they pull up the closest corresponding SmartAtlas slice with the ROI delineated. They can then use this to submit a query for any BIRN-accessible datasets (volumes, slices, high resolution EM, microarray, etc.).
USE CASE 4:
A researcher is interested in all BIRN-accessible datasets (volumes, slices, high resolution EM, microarray, etc.) around a nucleus in the cerebellum. They delineate this region in MBAT and submit a query that returns a list of all data from all sources in a format they may visualize using MBAT, a web page, or can download to their desktop.
USE CASE 5:
A researcher is looking at microarray gene expression data they have collected using MBAT. They begin to start examining the microarray data for normals compared to mouse models of Parkinson’s disease. They realize there seems to be something unusual in the caudate/putamen area in relation to gene lcn2. They would like to search the rest of the Mouse BIRN data for any images that:
- Show expression patterns for gene lcn2
- Were collected to study Parkinson’s disease
- Contain the caudate/putamen area
- Cell data collected within their delineated region of interest
They would generate this query in MBAT and this would bring up results showing the metadata from all BIRN-accessible data matching this query. They could then visualize the actual data (eventually through MBAT-overlaid on the atlas or their own data) either through a web-page link or they can download the data to their desktop.
USE CASE 6:
A researcher has a series of slices they have collected for an experiment on Schizophrenia. They have found what appears to be a very unusual formation in a part of the brain they are having a difficult time identifying. They decide to register these slices to the NT Atlas so they can visualize it, apply atlas delineations, to it and compare it to other normal datasets.
After registering the data, they use MBAT to access and open this dataset. Then they compare this volume to the corresponding NT atlas and MDA atlas for differences. They then switch off between applying the NT, MDA, and SmartAtlas delineations to it until they have found the most likely explanation for the unusual formation in their dataset.
They then delineate a portion of this area for any high-resolution datasets in normals in this area. They also do a search for any Schizophrenia-related data on the BIRN-accessible datasets.
| META FILEATTACHMENT | AtlasIntegrationScenarios?.doc | attr="" comment="Expanded version of Atlas Integration Scenarios" date="1121128250" moveby="jboline" movedto="MouseBIRN.AtlasingUseCases" movedwhen="1146075992" movefrom="MouseBIRN.MouseBIRNAtlasing" path="AtlasIntegrationScenarios.doc" size="45056" user="MaryannEMartone" version="1.2" |
|---|
|
