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Subpathway-GM

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A powerful analytical method for the identification of biologically meaningful metabolic subpathways. Subpathway-GM integrates ‘interesting genes’ and ‘interesting metabolites’ related to the study condition (e.g. disease) into the corresponding enzyme and metabolite nodes (referred to as signature nodes) within the metabolic pathway. We then analyzed lenient distance similarities of signature nodes within the pathway structure to locate key metabolic cascade subpathway regions. Finally, a hypergeometric test was used to evaluate the enrichment significance of these subpathway regions.

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Subpathway-GM forum

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Subpathway-GM classification

  • Animals
    • Homo sapiens

Subpathway-GM specifications

Interface:
Web user interface
Input data:
Users need to submit molecules of interest (genes and metabolites).
Stability:
Stable
Restrictions to use:
None
Computer skills:
Basic
Maintained:
Yes

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0 user reviews

No review has been posted.

Subpathway-GM forum

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No open topic.

Subpathway-GM versioning

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No versioning.

Subpathway-GM classification

  • Animals
    • Homo sapiens

Subpathway-GM specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Requirements:
graph, RBGL, igraph, XML, BiocGenerics
Maintained:
Yes

Subpathway-GM support

Documentation

Maintainer

  • Xia Li <>

Credits

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Publications

Institution(s)

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China

Funding source(s)

Funds for Creative Research Groups of the National Natural Science Foundation of China [81121003]; National Natural Science Foundation of China [61170154, 61073136, 81270511, 31200996 and 81000933]; Specialized Research Fund for the Doctoral Program of Higher Education of China [20102307120027 and 20102307110022]

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