Pathway Anaysis using IPA

Description about IPA:

• IPA stands for Ingenuity pathway analysis.
• It majorly deals with the creating molecular networks (algorithmically generated pathways).
• Dividing data into diseases and biological functions that are over represented in your data.
• Determining over represented signaling and metabolic canonical pathways.

There are actually 3 major aspects that can be taken from IPA

• Drug Interactions
• Growing/Generating a pathway
• Canonical Pathways

As my pet gene is CYP2C9 I had to find out if it is actually present in IPA for pathway analysis. Then I had to see if search it in IPA which would give a tabular form of data where I found my gene but there were no drug interactions associated to my gene.

Growing Pathway:

• I searched for CYP2C9 grew my pathway then created my pathway
• Add to my pathway—> build—> grow—> (direct/human/remove chemical molecule types and biologic drug)
• Then click on Apply.

• But in this scenario we could notice that there are only 10 molecules as 10 relationships in Direct association.
• So, we need to add some more pathways associated with CYP2C9 so that we can notice atleast of 20-25 relationships.

• So, the molecules being constant the number of relationships increased to 23.
• In case if there are more than 25 relationships we use "Trim" option to reduce the number of relationships.

•  We can see that there are no inhibitors and activators but definitely Protein-Protein interactions for an example between CYP2C9 and CYP2D6 etc.,

 

Canonical pathway:

•  Canonical actually mean the standard or unique pathway.
• In here I actually considered Xenobiotic metabolism as my canonical pathway.

• I want to explain the reason I choose this pathway that because the major disease associated with my gene is anti coagulation which is the reason for slow warfarin metabolism.

XENOBIOTICS

A xenobiotic is a foreign chemical substance found within an organism that is not normally naturally produced by or expected to be present within that organism. It can also cover substance which are present in much higher concentrations than are usual. Specifically, drugs such as antibiotics are xenobiotics in humans because the human body does not produce them itself, nor are they part of a normal food. 

 

•  Major genes associated to my pathway Xenobiotic metabolic signalling are CYP2C9 which is quite obvious I choose this pathway!! Inclusive to this we observe CYP3A4 and CYP2C. In the below figure we can see the disease associated to my pet gene. This gene plays a vital role in Deep vein thrombosis which is a disease associated with anti coagulation.