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This software consists of a curated database and several analysis tools to obtain pathways associated with a set of genes.
Using keywords of pathways or molecules, ChiBE can automatically query and obtain pathways from Pathway Commons through its web service.
Thus, by encoding measurement data into reaction-specific scores, one can obtain pathways which were active in the measured conditions, for instance.
If a suitable set of snapshots could be obtained and justified, enhanced MD sampling methods such as replica exchange could be applied to obtain pathways between bond addition cycle intermediates.
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The main aim of this study is to obtain pathway fractional integral operators associated with extended Mittag-Leffler functions.
This reduction strategy has also been used in other scenarios to obtain pathway activity indexes linked to the toxicological properties of chemical compounds [ 23].
With the help of the KEGG database, we can further study genes' biological complex behaviors, and by KEGG annotation we can obtain pathway annotation for unigenes.
In previous work, we used dimension reduction techniques to obtain pathway expression profiles, which are associated with a physiological outcome [ 22].
We obtained pathway and gene-level summary of associations by computing the adaptive combination of p-values.
We obtained pathway- and gene/region-based summary of associations using the adaptive combination of p-values [17], [18], which combines gene-level association evidence through adaptive rank truncated product method.
We obtained pathway information from the MSigDB v3.0 Canonical Pathways subset [ 54].
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