Introduction:

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database resource that integrates genomic, chemical and systemic functional information. Gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism, and the ecosystem. This tool implements the same algorithm of ‘metabolic pathway analysis’ modules of the popular MetaboAnalyst platform. The Number of libraries is increased to 67 and computing methods of network node importance is increased to 7.

The tool takes a compounds annotation file as input and performs pathway analysis based on information from KEGG.

Input files:

Compounds ID mapping results. Must be obtained from Tool: 'Compounds ID mapping'.

Parameter:

1. pathway library: 67 different species libraries have been provided, including Human, Mouse, Rat, Cow, Chicken, Zebrafish, Arabidopsis thaliana, Rice, Drosophila, Malaria, Budding yeast, E.coli., etc.

2. representation analysis algorithm:

hypergeometric test: In statistics, the hypergeometric test uses the hypergeometric distribution to calculate the statistical significance of having drawn a specific {\displaystyle k} k successes (out of {\displaystyle n} n total draws) from the aforementioned population. The test is often used to identify which subpopulations are over- or under-represented in a sample.

Fisher's exact test: It is a statistical significance test used in the analysis of contingency tables. The test is useful for categorical data that result from classifying objects in two different ways; it is used to examine the significance of the association (contingency) between the two kinds of classification.

3. Specify pathway topology analysis algorithm:

The module provides 7 popular topological measures found on the left-panel to

provide users greater insight into their networks.

Nodes with high scores in 7 measures are more likely to be important hubs.

Output files:

1. 'Pathway_Result.txt', KEGG pathway enrichment analysis result.

2. 'Pathway_Bubbleplot.pdf', KEGG pathway enrichment result visualization diagram.

3. 'Pathway_Barplot.pdf', KEGG pathway enrichment result visualization diagram.

Reference:

[1] Xia J, Wishart D S. Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst[J]. Nature Protocols, 2011, 6(6):743-760.

[2] Chong, J., et al. (2018) MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic acids research, 46, W486-w494. http://www.metaboanalyst.ca.