Is there any way to download the complete set of complex data at cutoff 600?
The entire network should be available from genecensus.org/intint. If you go to: http://bioinfo.mbb.yale.edu/genome/intint/supplementary.htm there are several links under “probabilistic interactomes” that contain gzipped archives of the data (the most complete being the “PIT” data). When you unzip and unpack the PIT archive, you will find one file for each yeast protein. Each of these files contains four columns. A partner protein in the first column, and then three likelihood ratios for this protein pair (i.e., the pair between the protein after which the file is named and the partner protein), first for the PIE data, then for the PIP data and finally, in the last column, for the PIT data. Thus, these data cover all (or most) of the possible protein pairs in yeast for all ranges of likelihood ratios. So, you can use these data to filter out the protein pairs that have likelihood ratios greater than a certain cutoff.
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