Dear Experts, I have two sets of genes and I want to compare the pathways between these two sets. What is the correct method to do so. Also how can I visualize the results . i.e Can you please suggest me a software that can visualize the pathways.
Thanks!
What do you mean by 2 sets of genes here? Please be a bit clear about the question. Are you interested in finding the pathways that comes up with the two gene list? There are multiple softwares to do that, without going into deep dig I would like to point you to the threads where you can find the useful resources for pathway analysis with gene lists take a look at here and here. There if you do not find what these can cater to you then you can also take a look at the following
The above are for biological pathways then there is also something called Gene ontology enrichment or gene set enrichment. You can take a look at this links here and here
Just out a bit of curiosity before doing any pathway analysis you should first take the gene lists and put them in any venn diagram generator to see the amount of overlap and exclusivity and then carry on with your pathway analysis either for the common set or the exclusive sets depending upon your biological question.
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what are you meaning by pathways? interaction? if it is the case I suggest you to have look to the stringDB database http://string-db.org/