※Coming soon!
Ⅱ Glycan Miner
GlycanMiner is a tool for mining 「α-closed frequent subtrees」[12] from a set of glycan structures,
based on the work by Hashimoto et al., 2008.
α-closed frequent subtrees is defined as those substructures within the input that frequently appear within a specified range.
The minimum frequency of appearance must be specified by the user via the minsup parameter.
Those substructures that appear in at least minsup number of input glycan structures will be included in the outout.
Furthermore, in order to avoid too many similar substructures in the results, the α-parameter is used to specify the amount of overlap,
and it is defined by the followind equation: support(P) ＜ max(α support(T); minsup),
where support(T) refers th the number of glycan structures in which substructure T appears,
and substructure T is a subtree of substructure P.
利用目的
GlycanMiner は、糖鎖構造が大量に生成された場合に、共通かつ有意に見つかる糖鎖の部分構造を探すために用いられます。
例えば、糖鎖アレイの場合、コントロールとターゲットとそれぞれに強く結合する糖鎖構造群が出力されます。
そうすると、コントロールとターゲットの糖鎖構造群を個別に実行し、α-closed frequent subtree の結果を比較できます。
一方、糖鎖の質量分析で得られたたくさんの糖鎖構造情報を解析し、特異的に現れる糖鎖の部分構造の分析にも用いることができます。
利用方法
1. There is one major text field for entering the glycan structures in KCF format.
This input can also be provided in a text file which can be loaded directly.
2. A value between 0 and 1 should be specified for the alpha parameter,
and the minimum number by which the resulting substructure should appear should be specified for minimum support.
FIGURE5.6 GlycanMiner の入力画面。
KCF 形式の糖鎖構造情報を入力またはファイルからロードする。 次にalpha に0～1 まで数字を、minimum support に数字をそれぞれ入力しGo mine ボタンを押すと解析結果が表示される。
FIGURE5.7 GlycanMiner の結果画面。
Note that it may take a few minutes for the results to be displayed as much computation is required. We are currently working on optimizing this process. In the results, each alpha-closed frequent subtree is ranked according to p-value, which is computed by comparing the support of a similar structure with the same components but randomized. The actual value of the structure's support is also displayed, along with the figure of the structure itself. A name to label each structure is also given.