If overexpression of protein A can rescue the growth defect caused by mutation in protein B, can I consider protein A is working downstream of protein B? If yes, why is it so?
Consider a signalling pathway. An event triggers another event downstream. Similarly,
It seems that over-expression of A is the trigger. From the statement it follows that A is upstream from B.
The other way around might be possible but the corresponding functional linkage need to identified. If I misunderstood the terminology then please excuse me.
There are standard pathway databases like KEGG, HSLS, Reactome, Pathway Commons, PANTHER etc..
Further, Pathguide contains information about 569 biological pathway related resources and molecular interaction related resources. http://www.pathguide.org/
In one of these databases there might be a query facility where you can specify both proteins (and possibly up/down stream info).