Clustering analysis of microarray data. (a) Unsupervised clustering of the microarray dataset was performed with the dChip software using standard settings considering all nonredundant probes with positive hybridization signal. The dataset includes microarray hybridization results from input and immunoprecipitation (IP) samples from three experiments with anti-U2AF65 antibody (U1 to U3) and two experiments with anti-PTB antibody (P1 and P2). Sample clustering defines a tree with two first level branches corresponding to input and IP samples. (b) Re-clustering analysis after clearing transcripts that were over-represented either in the inputs or in all immunoprecipitation samples. Sample clustering defines a tree with three first level branches corresponding to input, U2AF65, and PTB immunoprecipitation samples. For clustering analysis, the probe signal intensities for each mRNA are standardized to have mean 0 and standard deviation 1 across all samples. The color scale for mRNAs is presented as follows: red represents expression level above mean expression of a gene across all samples, black represents mean expression; and green represents expression lower than the mean. Because of the standardization, probe signal intensities most likely fall within [-3, 3]. PTB, polypyrimidine tract binding protein; U2AF, U2 small nuclear RNP auxiliary factor.