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Software for pathway analysis

classify candidate genes

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2 replies to this topic

#1 lipeiqiang78

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Posted 30 August 2013 - 07:26 AM

Hi,

 I want to classify more than 200 genes into appropriate signal passway. Which software can do this?

Thank you!

 



#2 PhalanxBio

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Posted 30 August 2013 - 08:33 AM

There are a number of tools that allow you to do this.  Ingenuity Pathway Analysis is a very powerful tool, but you'll need a subscription:

 

http://www.ingenuity.com/products/ipa

 

Some free online tools include:

 

DAVID Bioinformatics http://david.abcc.ncifcrf.gov/

 

Panther;http://www.pantherdb.org/genes/

 

There are definitely others.



#3 pcrman

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Posted 30 August 2013 - 09:46 AM

As suggested by PhalanxBio, you can use DAVID tool. Just upload your list of genes and assign the appropriate background set, enriched pathways will be returned to you. It is important to use appropriate background gene set. For example, if the list of genes are from an array study, the whole gene set on the array should be used as background set. By default, David use whole genome genes as background. 






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