Manipulating the MapViewer Display |
| Sample User Question
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Gather information about the EDN1 gene using the various maps. Try
adding and removing maps from the display, zooming in and out at various
levels, and changing the Master Map. Several sample questions that can
be answered using the MapViewer about this gene are given on the answer
slide. Try them out. More about the map types and their contents will
follow this exercise.
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| Analysis/Comments |
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When a user begins research on a particular gene and tries to obtain as much
information as possible, two good starting points are Entrez Gene
and MapViewer because they bring together information from many different
sources. Here are some examples of types of questions that can be answered:
- What is known about the function of the protein this gene produces?
- Locate a Unigene Cluster on the appropriate map. How many ESTs are in
this cluster? How well does it match with the corresponding exon on the Genes_seq map?
- Based on the Genes_seq map, approximately how many exons are in this gene?
- Are there any known repeat sequences within this gene? Which types?
- Locate some SNPs (single-nucleotide polymorphisms) in the EDN1 gene. Identify
the nucleotide change for one of the SNPs.
- Identify a sequence tagged site (STS) within this gene. What size PCR product is
made by the set of primers?
- Can you estimate the size of this gene in bps?
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| Flow Chart |
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MapView of EDN1 - Use the MapViewer to view the EDN1 gene..
- Maps and Options - Use this link to open the dialog box that allows you
to select which maps will be viewed, which map is the Master Map, which maps
have rulers displayed and other viewing options.
- Human Maps Help - Use the Human Maps Help link on the left blue sidebar to
identify which maps you need to find specific types of information.
- Entrez Gene - Clicking on
the name of a displayed gene will open the Entrez Gene record for that gene which will provide
various information including any known function for the gene's protein product.
- dbSNP - Clicking on the identifier
number of a SNP (rs#) on the Variation map will open the corresponding dbSNP record.
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| Step By Step Guide |
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- Link to the Entrez Gene record by clicking on "EDN1." It is a hormone released by neutrophils which is involved with
regulation of cell proliferation.
- Add the UgHs (Hs_UniG) map to the display to see the EST clusters.
- Zoom in closely on the EDN1 gene until you can distinguish thick from thin areas
in the blue line marking the gene. Count the thick areas (boxes) which represent the exons. There appear to be 5 exons.
This can be checked using the SV and EV links that will be discussed later in this
module.
- Add the repeats map to the display. Click on any of the map objects within the gene region to learn more about them.
- Add the variation map to the display. Click on any of the map objects within the gene region to learn more about them and identify
the base pair polymorphism.
- Add the STS map to the display. Click on any of the map objects within the gene region to learn more about them.
- Add a ruler to Genes_seq map. The gene appears to be approx. 6kb in size.
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| Additional Notes |
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