High-quality binary protein interaction map of the yeast interactome network.
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.
Yu
Haiyuan
H
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Braun
Pascal
P
Yildirim
Muhammed A
MA
Lemmens
Irma
I
Venkatesan
Kavitha
K
Sahalie
Julie
J
Hirozane-Kishikawa
Tomoko
T
Gebreab
Fana
F
Li
Na
N
Simonis
Nicolas
N
Hao
Tong
T
Rual
Jean-François
JF
Dricot
Amélie
A
Vazquez
Alexei
A
Murray
Ryan R
RR
Simon
Christophe
C
Tardivo
Leah
L
Tam
Stanley
S
Svrzikapa
Nenad
N
Fan
Changyu
C
de Smet
Anne-Sophie
AS
Motyl
Adriana
A
Hudson
Michael E
ME
Park
Juyong
J
Xin
Xiaofeng
X
Cusick
Michael E
ME
Moore
Troy
T
Boone
Charlie
C
Snyder
Michael
M
Roth
Frederick P
FP
Barabási
Albert-László
AL
Tavernier
Jan
J
Hill
David E
DE
Vidal
Marc
M
D019295:Computational Biology; D053263:Gene Regulatory Networks; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways; D040081:Protein Array Analysis; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods / Q000592:standards; D020543:Proteome / Q000378:metabolism; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism; D020798:Two-Hybrid System Techniques
D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors