Protein interaction mapping: a Drosophila case study.

By E. Formstecher, Sandra Aresta, V. Collura, A. Hamburger, Alain Meil, Alexandra Trehin, Céline Reverdy, V. Betin, Sophie Maire, C. Brun and 32 more. Genome Research, 2005

579 citations recorded by the source corpus.

The Drosophila (fruit fly) model system has been instrumental in our current understanding of human biology, development, and diseases. Here, we used a high-throughput yeast two-hybrid (Y2H)-based technology to screen 102 bait proteins from Drosophila melanogaster, most of them orthologous to human cancer-related and/or signaling proteins, against high-complexity fly cDNA libraries. More than 2300 protein-protein interactions (PPI) were identified, of which 710 are of high confidence. The computation of a reliability score for each protein-protein interaction and the systematic identification of the interacting domain combined with a prediction of structural/functional motifs allow the elaboration of known complexes and the identification of new ones. The full data set can be visualized using a graphical Web interface, the PIMRider (http://pim.hybrigenics.com), and is also accessible in the PSI standard Molecular Interaction data format. Our fly Protein Interaction Map (PIM) is surprisingly different from the one recently proposed by Giot et al. with little overlap between the two data sets. Analysis of the differences in data sets and methods suggests alternative strategies to enhance the accuracy and comprehensiveness of the post-genomic generation of broad-scale protein interaction maps.

Subfields: Computational Theory and Mathematics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/cab5e38bae135dce3da33b09174bb2be757095b6

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Citations in the corpus

Estimating the size of the human interactome (2008, methodology): “(36) were detailed and highly focused studies of cell regulation and cancer/signaling-related proteins in D. melanogaster , respectively; because only interactions among restricted sets of proteins were studied, these ﬁndings have resulted in very detailed but highly localized maps that result in…”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, unknown): “In contrast to the high throughput library screens used to analyze model organisms (Formstecher et al., 2005; Giot et al., 2003; Li et al., 2004), we have carried out a matrix interaction mating screen.”
FlyMine: an integrated database for Drosophila and Anopheles genomics (2007, unknown): “cerevisiae IntAct [65-74]*”
Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps (2007, result): “Similarly, comparison of two fly screens reveals few interactions in common [5,21].”
Interactome: gateway into systems biology. (2005, result): “screens for Drosophila showed minimal overlap with this larger study (103,104), echoing the situation seen for the two yeast studies.”
A human functional protein interaction network and its application to cancer data analysis (2010, background): “In addition, some pairwise interaction data sets may have high false positive rates [43,44], which contribute noise to the system, and interfere with pathway-based analyses.”
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans (2007, background): “The Nc protein, which has several roles including sperm individualization [94], may physically interact with products of at least eight other genes (Ice, Laminin A, tramtrack, BTB protein-VII, Apaf-1 related killer, Dodeca satellite binding protein 1, CG4282, and CG6767; see [107]).”
Global topological features of cancer proteins in the human interactome (2006, methodology): “, 2005), gene ontology (Formstecher et al., 2005), structural information (Dunker et al., 2005) and domain composition (Riley et al., 2005; Wuchty and Almaas, 2005). Studies focusing on the human interactome have thus far been limited due to lack of reliable and comprehensive experimental data. To c”
Yeast Two-Hybrid, a Powerful Tool for Systems Biology (2009, unknown): “Y2H can be easily automated for highthroughput studies of protein interactions on a genome-wide scale, as shown for viruses like bacteriophage T7 [18], Saccharomyces cerevisiae [19,20], Drosophila melanogaster [21], Caenorhabditis elegans [22] and humans [23,24].”
Organizing the Cell Cortex: The role of ERM proteins (2010, background): “The mechanism by which Moesin facilitates high levels of Hedgehog signalling is not clear; however, a previous yeast two-hybrid interaction study showed that Moesin interacts with Patche”