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Still, STRING contains information on thousands of protein interactions, including the most prominent and well-studied PIP interactors. Secondary interaction partners of these well-characterized PIP proteins are extensively described in the literature and therefore are present in the database. Importantly, STRING does not need to be comprehensive to assess the presence of secondary binding proteins in our data set. This secondary PIP interaction analysis, based upon experimental prediction methods and high-confidence STRING interactors (confidence score > 0.9 [von Mering et?al., 2005]), revealed that the vast majority of proteins identified in our PIP interactome are likely to be direct PIP interactors, since only a few functional interactions are recorded in STRING among the PIP-interacting proteins (Figure?S3). Pfam domain analysis revealed that PIP-interacting domains, such Bumetanide as the pleckstrin homology (PH) (Haslam et?al., 1993), calponin homology (CH) Alisertib cell line (Fukami et?al., 1996), RNA recognition motif (RBD) (Okada and Ye, 2009), and DOCK homology region (DHR) (C?t�� et?al., 2005) domains, were highly enriched among our identified PIP-interacting proteins (Figure?4B). Taken together, these data confirm that our approach permits a stringent and high-confidence identification of the PIP interaction proteome (Table S1). Next, we assessed the cellular distribution of identified PIP-interacting proteins and compared their distribution against the entire human proteome (Figure?4C). Surprisingly, a significant enrichment (p?this website functionally distinct subcellular compartments. Our data are consistent with emerging evidence that PIPs play important biological roles in the nucleus (Barlow et?al., 2010). To investigate whether interactors of any specific PIP might be enriched within the nucleus, we compared the distribution of the entire PIP interactome with its nuclear constituents (Figure?4D). PI(4)P interactors were significantly (p?
