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7.2 years ago
Learner
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Lets say I have a bunch of proteins which have interactions with each other. I want to know how to find the biological function of them all together and one by one
I appreciate any comment
That's an enormously broad question.
Bioinformatically speaking, your best bet, to my mind would be ontology analysis to see if it has known analogous proteins for which the functions are known. I think InterProScan gives you this kind of information back. Otherwise, look at the ontology databases for pathways etc.
If your proteins are unknown, then you can maybe get some information about domain searches etc. I really like HHPred and Pfam for this.
If you still get nothing, they you have to go and get your hands dirty in the lab.
@jrj.healey this is for each protein alone , right? for the analogous analysis, one should convert to gene, then it will be difficult to say something for a cluster of them, right? I did not know about HHPred, thanks I am going to give it a try
If you are interested in the function of a protein complex then this boils down to an overrepresentation analysis of the functions of the individual proteins, given that those are known. That's gene set enrichment analysis, many tools exist for this (commonly implementing a hypergeometric test). So roughly, if you find that 12 out of 15 genes in your complex are functioning in microtubule stabilisation, I think it's safe to assume your complex plays a role in microtubule stabilisation.
@WouterDeCoster where these numbers are coming from ? "find that 12 out of 15 genes". Do you know the concept of GSEA? I believe you should not write something you don't know because it confuses others.
He was giving you a hypothetical example. If you want people's help, I suggest you change your attitude.
Oh, wonderful reaction. Good luck figuring it out.