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Two of the proteins I am researching are known to interact. However, I would like to know if they interact with other proteins as well, and possibly form a pathway. Which analytical technique(s) I should use to determine this if I did all in silico analysis already? Any suggestion is welcome.

I am using a nematode C. elegans in my research, and RNAi is not an option, as I have already performed it.

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closed as too broad by MattDMo, kmm, AliceD, WYSIWYG Jan 17 '17 at 13:30

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. Avoid asking multiple distinct questions at once. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • $\begingroup$ This question is far too broad. From the help center: Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much. The field of protein-protein interactions is quite wide, and there are numerous techniques to consider. This is not the place to list all of them. $\endgroup$ – MattDMo Jan 14 '17 at 19:54
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There are plenty of methods to use. Here is a overview and background of some common methods as written by ThermoFisher:

https://www.thermofisher.com/se/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-protein-interaction-analysis.html

There is also phage display if you want to find binding partners, which is a very interesting method to narrow down binding partners from an entire interactome. It simple to set up in a lab and you can perform it all in a 96-well plate using ELISA and several rounds of phage selection. And of course there are also e.g. yeast-2-hybrid (Y2H) or co-immunoprecipitation (Co-IP).

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