High-throughput Protein Interactome Data: Minable or Not?

There is an emerging trend in post-genome biology to study the collection of thousands of protein interaction pairs (protein interactome) derived from high-throughput experiments. However, high-throughput protein interactome data, especially when derived from the Yeast 2-Hybrid (Y2H) method, have been generally believed to be irreproducible and unreliable, with an estimated high "noise ratio" of more than 50%. In this work, we performed a comprehensive study on approximately 70,000 protein interactions derived from a systematic yeast 2-hybrid (SY2H) method. We performed a comprehensive analysis of biases, reproducibility, statistical significance, and biologically significant patterns in this data set. Surprisingly, we found these protein interactions have a much higher quality. The data represented a comprehensive survey of the entire human proteome with no chromosomal location bias. The reproducibility rate of interactions among replicated searches was quite good, i.e., at...

• Type: Conference
• Year: 2004
• Where: KDD
• Authors: Jake Yue Chen, Andrey Y. Sivachenko, Lang Li
• Keywords: Data Mining, KDD 2004, Keywords Protein Interaction, Protein Interaction Pairs, Protein Interactions