STRING - Search Tool for the Retrieval of Interacting Proteins

Great!! There used to be another, older version of this on EMBL but it was more reliant on text matching. This version is far advanced of the previous site... already learned something too. So why are metastatic cancer genes always associated with synaptic plasticity genes? Evolution -- a neat surprise at every turn.

Cool site.

Well maybe.

How much should we trust "interactions" derived from text mining of papers? Frankly, even a lot of two hybrid data is of dubious biological relevance.

Sometimes more is less.

Sometimes more is indeed less - or perhaps rather less is more. I would thus like to point out two features of STRING:

1) All interactions have confidence scores associated with them. The typical interaction from a high-throughput yeast two-hybrid experiment would have a lower confidence score than one from a small-scale study. Similarly, interactions derived by automated literature mining will receive a very low confidence score unless it is supported by multiple papers. Low-confidence interactions can easily be eliminated from an interaction network by specifying a cutoff for the confidence score.

2) It is possible to entirely turn off particular types of evidence. If, for example, text-mining results are unwanted (even those of high confidence) then one can simply turn of the text-mining channel.

This was really helpful and interesting.