Protein interaction mapping: A Drosophila case study
Etienne Formstecher,Sandra Aresta,Vincent Collura,Alexandre Hamburger,Alain Meil,Alexandra Trehin,Céline Reverdy,Virginie Betin,Sophie Maire,Christine Brun,Bernard Jacq,Monique Arpin,Yohanns Bellaïche,Saverio Bellusci,Philippe Benaroch,Michel Bornens,Roland Chanet,Philippe Chavrier,Olivier Delattre,Valérie Doye,Richard G. Fehon,Richard G. Fehon,Gérard Faye,Thierry Galli,Jean-Antoine Girault,Bruno Goud,Jean de Gunzburg,Ludger Johannes,Marie-Pierre Junier,Vincent Mirouse,Ashim Mukherjee,Dora Papadopoulo,Franck Perez,Anne Plessis,Carine Rossé,Simon Saule,Dominique Stoppa-Lyonnet,Alain Vincent,Michael A. White,Pierre Legrain,Jérôme Wojcik,Jacques Camonis,Jacques Camonis,Laurent Daviet +43 more
TLDR
This work 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.Abstract:
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.read more
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Towards a proteome-scale map of the human protein–protein interaction network
Jean François Rual,Kavitha Venkatesan,Tong Hao,Tomoko Hirozane-Kishikawa,Amélie Dricot,Ning Li,Gabriel F. Berriz,Francis D. Gibbons,Matija Dreze,Nono Ayivi-Guedehoussou,Niels Klitgord,Christophe Simon,Mike Boxem,Stuart Milstein,Jennifer Rosenberg,Debra S. Goldberg,Lan V. Zhang,Sharyl L. Wong,Giovanni Franklin,Siming Li,Joanna S. Albala,Joanna S. Albala,Janghoo Lim,Carlene Fraughton,Estelle Llamosas,Sebiha Cevik,Camille Bex,Philippe Lamesch,Robert S. Sikorski,Jean Vandenhaute,Huda Y. Zoghbi,Alex Smolyar,Stephanie Bosak,Reynaldo Sequerra,Lynn Doucette-Stamm,Michael E. Cusick,David E. Hill,Frederick P. Roth,Marc Vidal +38 more
TL;DR: An initial version of a proteome-scale map of human binary protein–protein interactions is described, which increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins.
Journal ArticleDOI
A human protein-protein interaction network : a resource for annotating the proteome
Ulrich Stelzl,Uwe Worm,Maciej Lalowski,Christian Haenig,Felix H. Brembeck,Heike Goehler,Martin Stroedicke,Martina Zenkner,Anke Schoenherr,Susanne Koeppen,Jan Timm,Sascha Mintzlaff,Claudia Abraham,Nicole Bock,Silvia Kietzmann,Astrid Goedde,Engin Toksöz,Anja Droege,Sylvia Krobitsch,Bernhard Korn,Walter Birchmeier,Hans Lehrach,Erich E. Wanker +22 more
TL;DR: A large, highly connected network of interacting pairs of human proteins was identified, characterizing ANP32A and CRMP1 as modulators of Wnt signaling and two novel Axin-1 interactions were validated experimentally.
Journal ArticleDOI
Organizing the cell cortex: the role of ERM proteins
TL;DR: The ERM proteins (ezrin, radixin and moesin) have a crucial role in organizing membrane domains through their ability to interact with transmembrane proteins and the cytoskeleton and can provide structural links to strengthen the cell cortex and regulate the activities of signal transduction pathways.
Journal ArticleDOI
The model organism as a system: integrating 'omics' data sets.
TL;DR: Researchers are rising to the challenge by using omics data integration to address fundamental biological questions that would increase the understanding of systems as a whole.
Journal ArticleDOI
Estimating the size of the human interactome
Michael P. H. Stumpf,Thomas Thorne,Eric de Silva,Ron Stewart,Hyeong Jun An,Michael Lappe,Carsten Wiuf +6 more
TL;DR: It is found that the human interaction network is one order of magnitude bigger than the Drosophila melanogaster interactome and ≈3 times bigger than in Caenorhabditis elegans.
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TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.
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