Pathway Enrichment analysis using IntPath

It is very fast to check say using IntPath (Zhou et al. ) just by input the gene list (in official symbol) and the database will return you a list of enriched pathways.

Currently IntPath is the most comprehensive database for pathway enrichment and can find more than other database do. So I would suggest the authors to have a look on that if possible.

How to use:
With the rapid development of MicroArray, RNAseq, PPIs, etc... many researchers ended up with a long list of proteins/genes (for example, deferentially expressed genes), and they ask what function/pathway/biological meaning are the list of genes related to? Here comes to the standard "pathway enrichment analysis" basically tell which pathways are this gene list close related to?

IntPath has very powerful and convenient function to do pathway enrichment analysis. Called "Identify Pathways". Click "Identify Pathways" and you will find the web interface.

(1) Choose the organisms, for example Homo Sapiens, 
(2) Input your gene list, Important! Please input the correct ID format! Most people failed here. The unified IntPath gene ID for Homo Sapiens is HGNC Symbol, Mus musculus is MGI Symbol, Saccharomyces cerevisiae is Systematic name, and Mycobacterium tuberculosis H37Rv is TuberList Rv number. 
(3) Choose your p-value threshold, only the results with p-value lower than this will be displayed.
(4) Submit.
(5) Results will be directly displayed on the web interface, if it is a long list, it can take  10~30 mins to finish the calculation. IntPath is build on an old server.

Usage Example:

(1)I have a list of genes as follows:
GPR15
MIR155
IRF2BP2
DUSP22
STK24
ZFP36L1
RFTN1
DUSP22
ISCU
MYC

(2)Then according to the above instruction, I have pasted this list on the "Identify Pathways" page.

(3)Then, I click click and I get the results. With p-value displayed. We can see it is strong cancer related gene list with enrichment in following 3 pathways.

(4)Sometimes, you have lots of results output with small p-values, you can choose the results with the smallest p-value as the most relevant pathways enriched.

Enjoy the most comprehensive and accurate pathway enrichment analysis powered by IntPath!

If you have any questions, be free to contact the author of IntPath, Dr. Hufeng Zhou.
zhouhufeng(AT)gmail.com

Reference:
[1]Hufeng Zhou, Jingjing Jin, Haojun Zhang, Bo Yi, Michal Wozniak, and Limsoon Wong. "IntPath--an integrated pathway gene relationship database for model organisms and important pathogens." BMC systems biology 6, no. Suppl 2 (2012): S2.