Should you only use significant proteins when performing pathway analysis or your whole dataset (after filtering etc)?

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Busari Yusuf

For you to know the pattern of changes, all the proteins mist be included and even for the sake of analysis.

Jochen Wilhelm

Apart from the problem that it is not well defined what is meant with "significant", you will likey get a very biased picture if you work with some selection (selected by siginficance or whatever else). So you better should use all the data.