Today we will be looking at the program IPA and some of what it can accomplish. IPA is a program that is amazing for mapping out pathways and finding connections between genes or proteins. For our exercise we are going to be looking at ASPA and some of its associated connections. IPA also gives you a lot of secondary information about what you want to know. I found that there are no drugs currently associated with ASPA. Below is an example of a pathway that you can build with IPA. ASPA appears to be an understudied protein or not very active because when I limited the pathway to humans IPA did not find any connections. Only when I included multiple species and kept indirect interactions checked did I start to find connections. The two indirect connections are casein and FOLR1
According to the pathway 11 inhibitors, 2 activator and 2 protein-protein interaction molecules are connected to ASPA. The 11 inhibitors are miRNA which are small noncoding RNA that are used to regulate gene expression. The two activators are enzymes that are used to catalyze a chemical reactions. One protein-protein interaction molecule is a transporter and the other is involved in a few different functions.
In the picture below you can see IPA gave the location of each molecule on the pathway. A majority of the nodes are found in the cytoplasm. This makes sense because all the miRNA would be found where their complimentary mRNA are found. As for the two enzymes, aminoacylase and aspartoacylase, IPA has placed them in other. This is because to IPA the cellular location is unknown. FOLR1 can be found in the plasma membrane because it is a transporter. A side note is FOLR1 may be a cofactor for virus entry into some cells. This includes the filovirus family which Ebola is part of. Casein is in the other category. This probably because there are multiple types of casein found in many different areas.
Canonical Pathway
Another feature of IPA is canonical pathways. This lists all the canonical pathways that the genes on your pathway exist in. IPA does not have a canonical pathway for ASPA so I will have to use casein. Casein is involved in the Prolactin Signaling pathway. This is a very broad pathway that is involve in six main areas “reproduction and lactation, growth and development, endocrinology and metabolism, brain and behaviour, immunomodulation and osmoregulation”. The pathway begins with the secretion of the hormone prolactin from the pituitary glands. Prolactin itself is involved in more that 300 separate effects. As you can see in the picture below casein or more specifically casein beta is involve in the lactation process.
michelconn 