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About CSM
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The Composite Structure Map (CSM) is a merged tree of GLYCAN
structures containing all possible variations of carbohydrate structures.
Push the 'Go' button to display the map.
The most right node is the root of the structures, representing a
carbohydrate structure of one monosaccharide, say glucose.
This root node is connected to the nodes
to its left at the 2nd level from the right, which represent possible
structures of two monosaccharides containing glucose as the single core.
Nodes connected at each consecutive level represent these variations
iteratively. Because every type of glycosidic linkage is distinguished,
different
glycosidic linkages are represented by different edges even if the
attached monosaccharides are the same. For example, when a Gal can be
attached to Glc by a b1-3 and a b1-4 glycosidic linkage, the CSM will
contain two different edges 'Gal(b1-3)Glc' and 'Gal(b1-4)Glc.'
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Selecting organism
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Selecting an organism from the pull-down menu at the top
changes the hyperlinks to the edges on the map.
For example, after selecting 'All organisms in KEGG' and pushing the
'Go' button, edges that (1) correspond to glycosyltransferases that
catalyze the synthesis of that structure and (2) have
references in KO will be hyperlinked to its corresponding KO entry.
On the other hand, if a particular organism is selected under the
same pull-down menu, the edges will be hyperlinked to the genes
corresponding to the selected organism.
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Display options
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Selecting three monosaccharides in the three
pull-down menus labeled 'Root,' 'Next1,' 'Next2' will display the CSM
that containing the designated chain of monosaccharides as its core.
Other parameters to adjust the visualized contents in the tree are also available.
For example, a "Threshold" value may be specified to indicate
the minimum number of times a particular edge
should appear in the tree in order to be displayed.
The "Position" may be adjusted to display the CSM with the root
at the top, the right (default), the left, or the bottom.
The "Node size" may be adjusted to increase the displayed size of
the nodes in the CSM from the default minimum value of 5.
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Superimposing microarray data
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Moreover, other functionality such as visualizing microarray
results is under development.
Download and then upload the sample data at the bottom and
see the coloring of edges.
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