WI‐PHI: A weighted yeast interactome enriched for direct physical interactions
- 16 March 2007
- journal article
- research article
- Published by Wiley in Proteomics
- Vol. 7 (6), 932-943
- https://doi.org/10.1002/pmic.200600448
Abstract
How is the yeast proteome wired? This important question, central in yeast systems biology, remains unanswered in spite of the abundance of protein interaction data from high-throughput experiments. Unfortunately, these large-scale studies show striking discrepancies in their results and coverage such that biologists scrutinizing the “interactome” are often confounded by a mix of established physical interactions, functional associations, and experimental artifacts. This stimulated early attempts to integrate the available information and produce a list of protein interactions ranked according to an estimated functional reliability. The recent publication of the results of two large protein interaction experiments and the completion of a comprehensive literature curation effort has more than doubled the available information on the wiring of the yeast proteome. This motivates a fresh approach to the compilation of a yeast interactome based purely on evidence of physical interaction. We present a procedure exploiting both heuristic and probabilistic strategies to draft the yeast interactome taking advantage of various heterogeneous data sources: application of tandem affinity purification coupled to MS (TAP-MS), large-scale yeast two-hybrid studies, and results of small-scale experiments stored in dedicated databases. The end result is WI-PHI, a weighted network encompassing a large majority of yeast proteins.Keywords
This publication has 39 references indexed in Scilit:
- Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeNature, 2006
- Proteome survey reveals modularity of the yeast cell machineryNature, 2006
- BioGRID: a general repository for interaction datasetsNucleic Acids Research, 2006
- Evidence for dynamically organized modularity in the yeast protein–protein interaction networkNature, 2004
- IntAct: an open source molecular interaction databaseNucleic Acids Research, 2004
- Global analysis of protein localization in budding yeastNature, 2003
- Comparative assessment of large-scale data sets of protein–protein interactionsNature, 2002
- Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryNature, 2002
- Functional organization of the yeast proteome by systematic analysis of protein complexesNature, 2002
- A comprehensive two-hybrid analysis to explore the yeast protein interactomeProceedings of the National Academy of Sciences of the United States of America, 2001