Proteins whose expression is altered by the expression of four or more oncogenes.

Proteins shown are those where a confident assessment of a common decrease or increase in 4 or more of the 6 oncogenes has been found. To be included the protein must be called as changing in the majority of experiments in which it is quantified and must not be called as changing in the internal replicate. To be called as changing a protein must have a ratio outside the range in which 95% of protein ratios for the internal replicate are found and a p-value of 0.05 or less. The ratio column contains an average of the ratios across multiple experiments. This is supported by the averaged confidence which indicates how closely the experiments agree. The confidence for each experiment is the proportion of ratios in the internal replicate that the ratio in question is outside of. (So the value for an ‘Up’ call is between 0.95 and 0.99 inclusive). This gives a normalised value between −0.99 and 0.99 for each experiment. A value of greater magnitude indicates more agreement between experiments supporting the change call. Values in brackets in the confidence column are those not called as changing.