David M. Sander" <dmsander at mailhost.tcs.tulane.edu> writes:
>I am interested in obtaining a map of mouse chromosome 11. Does anyone
>know where this could be obtained either in a database or other form?
There is a gopher version of the The Encyclopedia of the Mouse Genome.
Here you can view the genetic maps of each mouse chromosome, search
for specific loci on these maps as well as search for references and
notes associated with each locus on the map.
In addition you can search the Mouse Locus Catalog which contains detailed
information on mouse loci.
Now for a little tour:
Point your gopher client at merlot.welch.jhu.edu and select the following:
--> 13. Search Databases at Hopkins (Vectors, Promoters, NRL-3D, EST, OMIM../
--> 17. Mouse Databases (TBASE, Encyclopedia of the Mouse Genome)/
--> 1. Encyclopedia of the Mouse Genome/
And you'll see:
--> 1. About the Encyclopedia of the Mouse Genome.
2. Browse through the Chromosomes/
3. Search Maps for Loci <?>
4. Notes <?>
5. References <?>
6. Mouse Locus Catalog (MLC) <?>
If you have a specific locus in mind that you would like to see it's map
position select:
--> 3. Search Maps for Loci <?>
If you want to see the map position of abl:
+--------------------------Search Maps for Loci--------------------------+
| _____________________________ |
| Words to search for | abl | |
| ----------------------------- |
| [Cancel ^G] [Accept - Enter] |
| |
+------------------------------------------------------------------------+
And you'll see:
--> 1. Abl - Abelson murine leukemia oncogene (2)
If you select this entry you will see the map for Chromosome 2 with the
Expanded view which contains Abl.
Note that above you are shown the Locus symbol, Abl, the locus name, Abelson
murine leukemia oncogene, and the Chromosome on which it resides, (2). These
are all searchable. For example your could search for:
+--------------------------Search Maps for Loci--------------------------+
| _____________________________ |
| Words to search for | leukemia and 2 | |
| ----------------------------- |
| [Cancel ^G] [Accept - Enter] |
| |
+------------------------------------------------------------------------+
And you'll see:
--> 1. Abl - Abelson murine leukemia oncogene (2)
2. Glvr-1 - gibbon ape leukemia virus receptor-1 (2)
3. Mpmv-14 - modified polytropic murine leukemia virus-14 (2)
4. Mpmv-28 - modified polytropic murine leukemia virus-28 (2)
5. Mpmv-3 - modified polytropic murine leukemia virus-3 (2)
6. Mpmv-43 - modified polytropic murine leukemia virus-43 (2)
7. Pmv-33 - polytropic murine leukemia virus-33 (2)
8. Pmv-63 - polytropic murine leukemia virus-63 (2)
9. Pmv-7 - polytropic murine leukemia virus-7 (2)
10. Xmmv-71 - xenotropic-MCF leukemia virus-71 (2)
11. Xmv-10 - xenotropic murine leukemia virus-10 (2)
12. Xmv-48 - xenotropic murine leukemia virus-48 (2)
You may use booleans (and, or, not) and wildcards (*) to broaden or narrow
your searches.
--------------------
If you would like the notes and references associated with each
locus select:
--> 4. Notes <?>
--> 5. References <?>
You can search for loci, authors or journals. You may use booleans (and, or,
not), phrase searches ("...") and wildcards (*) to broaden or narrow your
searches.
--------------------
If you would like detailed information on a locus or to search for loci
by topic select:
--> 6. Mouse Locus Catalog (MLC) <?>
and for example search for:
+--------------------------Mouse Locus Catalog (MLC)---------------------+
| _____________________________ |
| Words to search for | leukemia and 2 | |
| ----------------------------- |
| [Cancel ^G] [Accept - Enter] |
| |
+------------------------------------------------------------------------+
And you will see:
1. LOCUS Igf1r locus, insulin-like growth factor 1 receptor. ...
--> 2. LOCUS Insr locus, insulin receptor. CHROMOSOME 8 CLA...
3. LOCUS Igf2r locus, insulin-like growth factor II receptor. ...
A sample entry is as follows:
--------------------------------------------------------------------------
LOCUS
Insr locus, insulin receptor.
CHROMOSOME
8
CLASSES
Receptors
TEXT
Insr locus, insulin receptor, Chr 8. The transmembrane
allosteric enzyme which acts as an insulin receptor is composed
of alpha and beta subunits. Both are thought to be derived through
the cleavage of a common proreceptor precursor. When insulin
interacts with its binding site on the extracellular alpha subunit,
a cytoplasmic tyrosine kinase domain in the beta subunit is
activated (3). The Insr gene in the mouse has been localized to
the proximal end of Chr 8, using somatic cell hybrids (4) and
two interspecific backcrosses (1, 2). See also the
insulin-like growth factors (Igf-) and their receptors.
REFERENCES
1. Ceci, J.D., M.L. Justice, L.F. Lock, N.A. Jenkins, and
N.G. Copeland. 1990. An interspecific backcross linkage
map of mouse Chromosome 8. Genomics 6:72-79.
2. Howard, T.A., J.M. Rochelle, A.M. Saunders, and M.F.
Seldin. 1991. A linkage map of mouse Chromosome 8:
further definition of the syntenic relationship between
mouse Chromosome 8 and human Chromosomes 8, 16 and 19.
Genomics 10:207-213.
3. Sibley, E., T. Kastelic, T.J. Kelly, and M.D. Lane.
1989. Characterization of the mouse insulin receptor
gene promoter. Proc. Natl. Acad. Sci. USA 86:9732-9736.
4. Wang, L.-M., A.M. Killary, X.-E. Fang, S. K. Parriott,
P.A.Lalley, G.I. Bell, and A.Y. Sakaguchi. 1988.
Chromosome assignment of mouse insulin, colony
stimulating factor 1, and low-density lipoprotein
receptors. Genomics 3:172-175.
UPDATED
Wed May 13 14:59:40 EDT 1992
TAG
Insr
----------------------------------------------------------------------
If you would simply like to browse through the Maps select:
--> 2. Browse through the Chromosomes/
And you will see:
--> 1. Chromosome 1/
2. Chromosome 2/
3. Chromosome 3/
4. Chromosome 4/
5. Chromosome 5/
6. Chromosome 6/
7. Chromosome 7/
8. Chromosome 8/
9. Chromosome 9/
10. Chromosome 10/
11. Chromosome 11/
12. Chromosome 12/
13. Chromosome 13/
14. Chromosome 14/
15. Chromosome 15/
16. Chromosome 16/
17. Chromosome 17/
18. Chromosome 18/
19. Chromosome 19/
20. Chromosome X/
21. Chromosome Y/
Now select the Chromosome that you are interested in browsing
lets try Chromosome 1 - you will see:
--> 1. Overview of Chromosome 1
2. Expanded View 1 (Region 5-7)
3. Expanded View 2 (Region 10-11)
4. Expanded View 3 (Region 15-21)
5. Expanded View 4 (Region 23-30)
6. Expanded View 5 (Region 31-40)
7. Expanded View 6 (Region 41-47)
8. Expanded View 7 (Region 48-54)
9. Expanded View 8 (Region 55-59)
10. Expanded View 9 (Region 60-68)
11. Expanded View 10 (Region 69-77)
12. Expanded View 11 (Region 79-81)
13. Expanded View 12 (Region 82-87)
If you select "Overview of Chromosome 1" you will see a simple
map containing some loci and with a number scale running down
the left side of the map:
|
10 |
|
20 |
|
30 |
|
40 |
|
50 |
|
60 |
|
70 |
|
80 |
|
90 |
|
100|
|
|
Use the numbers to define the Region where you would like to see an Expanded
view of the map - which will show all the loci present in that section.
==============================================================================
If you've never heard of gopher, don't worry - it's free and on the net.
Write me a note if you'd like information on how to get started.
To view the maps in the Encyclopedia you need to be able to display
images. Many of the gopher clients will work just fine - a few
hints:
If you're using a Mac - go get the latest version of Turbogopher (earlier
versions had trouble launching lin
