Empirically controlled mapping of the Caenorhabditis  elegans protein-protein interactome network.
To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards.We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of approximately 10,000 x approximately 10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at approximately 116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins
Simonis
Nicolas
N
Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
Rual
Jean-François
JF
Carvunis
Anne-Ruxandra
AR
Tasan
Murat
M
Lemmens
Irma
I
Hirozane-Kishikawa
Tomoko
T
Hao
Tong
T
Sahalie
Julie M
JM
Venkatesan
Kavitha
K
Gebreab
Fana
F
Cevik
Sebiha
S
Klitgord
Niels
N
Fan
Changyu
C
Braun
Pascal
P
Li
Ning
N
Ayivi-Guedehoussou
Nono
N
Dann
Elizabeth
E
Bertin
Nicolas
N
Szeto
David
D
Dricot
Amélie
A
Yildirim
Muhammed A
MA
Lin
Chenwei
C
de Smet
Anne-Sophie
AS
Kao
Huey-Ling
HL
Simon
Christophe
C
Smolyar
Alex
A
Ahn
Jin Sook
JS
Tewari
Muneesh
M
Boxem
Mike
M
Milstein
Stuart
S
Yu
Haiyuan
H
Dreze
Matija
M
Vandenhaute
Jean
J
Gunsalus
Kristin C
KC
Cusick
Michael E
ME
Hill
David E
DE
Tavernier
Jan
J
Roth
Frederick P
FP
Vidal
Marc
M
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D006801:Humans; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software
D029742:Caenorhabditis elegans Proteins