To test for clustering, pairs on points on the tSNE plot were binned by separation, and the autocorrelation at distance r was calculated as the average product of fold changes for the pairs of proteins in bin r divided by the variance of all proteins showing significant change. Smooth fits of exponentials allowing free parameters for amplitude and decay length were carried out. P values were derived from random permutations of the data 1000 times in each comparison, with the null hypothesis that the exponential fit should have amplitude and decay length as long as that in the observed data. Scripts to generate Figs. 2 (D and E) and 3 (A to E) and fig. S3 (C to F) will be made available online.

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