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[71] Walhout AJ, Boulton SJ, et al. Yeast two-hybrid systems and
protein interaction mapping projects for yeast and worm. Yeast
2000;17(2):88 e 94.
[72] Grove CA, De Masi F, et al. A multiparameter network reveals
extensive divergence between C. elegans bHLH transcription
factors. Cell 2009;138(2):314 e 27.
[73] Lamesch P, Li N, et al. hORFeome v3.1: a resource of human
open reading frames representing over 10,000 human genes.
Genomics 2007;89(3):307 e 15.
[74] Rual JF, Hirozane-Kishikawa T, et al. Human ORFeome version
1.1: a platform for
[93] Lage K, Karlberg EO, et al. A human phenome-interactome
network of protein complexes implicated in genetic disorders. Nat
Biotechnol 2007;25(3):309 e 16.
[94] Wang PI, Marcotte EM. It's the machine that matters: predicting
gene function and phenotype from protein networks. J Proteomics
2010;73(11):2277 e 89.
[95] Beck M, Schmidt A, et al. The quantitative proteome of a human
cell line. Mol Syst Biol 2011;7:549.
[96] Ghaemmaghami S, Huh WK, et al. Global analysis of protein
expression in yeast. Nature 2003;425(6959):737 e 41.
[97] Aebersold R, Mann M. Mass spectrometry-based proteomics.
Nature 2003;422(6928):198 e 207.
[98] Gingras AC, Gstaiger M, et al. Analysis of protein complexes
using mass spectrometry. Nat Rev Mol Cell Biol 2007;8(8):
645 e 54.
[99] Kocher T, Superti-Furga G. Mass spectrometry-based functional
proteomics: from molecular machines to protein networks. Nat
Methods 2007;4(10):807 e 15.
[100] Puig O, Caspary F, et al. The tandem affinity purification (TAP)
method: a general procedure of protein complex purification.
Methods 2001;24(3):218 e 29.
[101] Burckstummer T, Bennett KL, et al. An efficient tandem affinity
purification procedure for interaction proteomics in mammalian
cells. Nat Methods 2006;3(12):1013
reverse proteomics. Genome Res 2004;
14(10B):2128 e 35.
[75] D'Haeseleer P, Church GM. Estimating and improving protein
interaction error rates. Proc IEEE Comput Syst Bioinform Conf
2004:216 e 23.
[76] Grigoriev A. On the number of protein e protein interactions in the
yeast proteome. Nucleic Acids Res 2003;31(14):4157 e 61.
[77] Hart GT, Ramani AK, et al. How complete are current yeast
and human protein-interaction networks? Genome Biol 2006;
7(11):120.
[78] Huang H, Jedynak BM, et al. Where have all the interactions
gone? Estimating the coverage of two-hybrid protein interaction
maps. PLoS Comput Biol 2007;3(11):e214.
[79] Reguly T, Breitkreutz A, et al. Comprehensive curation and
analysis of global interaction networks in Saccharomyces cer-
evisiae. J Biol 2006;5(4):11.
[80] Sambourg L, Thierry-Mieg N. New insights into protein
9.
[102] de Boer E, Rodriguez P, et al. Efficient biotinylation and single-
step purification of tagged transcription factors in mammalian
cells and transgenic mice. Proc Natl Acad Sci U S A 2003;
100(13):7480 e 5.
[103] Glatter T, Wepf A, et al. An integrated workflow for charting the
human interaction proteome: insights into the PP2A system. Mol
Syst Biol 2009;5:237.
[104] Ho Y, Gruhler A, et al. Systematic identification of protein
complexes in Saccharomyces cerevisiae by mass spectrometry.
Nature 2002;415(6868):180 e 3.
[105] Poser I, Sarov M, et al. BAC TransgeneOmics: a high-throughput
method for exploration of protein function in mammals. Nat
Methods 2008;5(5):409 e 15.
[106] Rigaut G, Shevchenko A, et al. A generic protein purification
method for protein complex characterization and proteome
exploration. Nat Biotechnol 1999;17(10):1030 e 2.
[107] Guruharsha KG, Rual JF, et al. A protein complex network of
Drosophila melanogaster. Cell 2011;147(3):690 e 703.
[108] Bader GD, Hogue CW. An automated method for finding
molecular complexes in large protein interaction networks. BMC
Bioinformatics 2003;4:2.
[109] Choi H, Larsen B, et al. SAINT: probabilistic scoring of affinity
purification-mass spectrometry data. Nat Methods 2011;8(1):
70 e 3.
[110] Hart GT, Lee I, et al. A high-accuracy consensus map of yeast
protein complexes reveals modular nature of gene essentiality.
BMC Bioinformatics 2007;8:236.
[111] Hu P, Janga SC, et al. Global functional atlas of Escherichia coli
encompassing previously uncharacterized proteins. PLoS Biol
2009;7(4):e1000096.
[112] Kuhner S, van Noort V, et al. Proteome organization in a genome-
reduced bacterium. Science 2009;326(5957):1235 e 40.
[113] Behrends C, Sowa ME, et al. Network organization of the human
autophagy system. Nature 2010;466(7302):68 e 76.
e
protein
interaction data lead to increased estimates of the S. cerevisiae
interactome size. BMC Bioinformatics 2010;11:605.
[81] Sprinzak E, Sattath S, et al. How reliable are experimental protein e
protein interaction data? J Mol Biol 2003;327(5):919 e 23.
[82] Stumpf MP, Thorne T, et al. Estimating the size of the human
interactome. Proc Natl Acad Sci U S A 2008;105(19):6959 e 64.
[83] Worseck JM, Grossmann A, et al. A stringent yeast two-hybrid
matrix screening approach for protein e protein interaction
discovery. Methods Mol Biol 2012;812:63 e 87.
[84] Braun P, Tasan M, et al. An experimentally derived confidence
score for binary protein e protein interactions. Nat Methods 2009;
6(1):91 e 7.
[85] Chen YC, Rajagopala SV, et al. Exhaustive benchmarking of the
yeast two-hybrid system. Nat Methods 2010;7(9):667 e 8.
[86] Alberts B. The cell as a collection of protein machines: preparing
the next generation of molecular biologists. Cell 1998;92(3):
291 e 4.
[87] Gavin AC, Bosche M, et al. Functional organization of the yeast
proteome by systematic analysis of protein complexes. Nature
2002;415(6868):141 e 7.
[88] Kuriyan J, Eisenberg D. The origin of protein interactions and
allostery in colocalization. Nature 2007;450(7172):983
e
90.
[89] Williamson JR. Cooperativity in macromolecular assembly. Nat
Chem Biol 2008;4(8):458
e
65.
[90] Fraser HB, Plotkin JB. Using protein complexes to predict
phenotypic effects of gene mutation. Genome Biol 2007;8(11):
R252.
[91] Gavin AC, Aloy P, et al. Proteome survey reveals modularity of
the yeast cell machinery. Nature 2006;440(7084):631 e 6.
e
[92]
Ideker T, Sharan R. Protein networks in disease. Genome Res
2008;18(4):644 e 52.
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