An empirical framework for binary interactome mapping.
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains approximately 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal.
Venkatesan
Kavitha
K
Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.
Rual
Jean-François
JF
Vazquez
Alexei
A
Stelzl
Ulrich
U
Lemmens
Irma
I
Hirozane-Kishikawa
Tomoko
T
Hao
Tong
T
Zenkner
Martina
M
Xin
Xiaofeng
X
Goh
Kwang-Il
KI
Yildirim
Muhammed A
MA
Simonis
Nicolas
N
Heinzmann
Kathrin
K
Gebreab
Fana
F
Sahalie
Julie M
JM
Cevik
Sebiha
S
Simon
Christophe
C
de Smet
Anne-Sophie
AS
Dann
Elizabeth
E
Smolyar
Alex
A
Vinayagam
Arunachalam
A
Yu
Haiyuan
H
Szeto
David
D
Borick
Heather
H
Dricot
Amélie
A
Klitgord
Niels
N
Murray
Ryan R
RR
Lin
Chenwei
C
Lalowski
Maciej
M
Timm
Jan
J
Rau
Kirstin
K
Boone
Charles
C
Braun
Pascal
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Cusick
Michael E
ME
Roth
Frederick P
FP
Hill
David E
DE
Tavernier
Jan
J
Wanker
Erich E
EE
Barabási
Albert-László
AL
Vidal
Marc
M
D030562:Databases, Protein; D006801:Humans; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism*; D012680:Sensitivity and Specificity
D011506:Proteins