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Towards a proteome-scale map of the human protein–protein interaction network


Systematic mapping of protein–protein interactions, or ‘interactome’ mapping, was initiated in model organisms, starting with defined biological processes1,2 and then expanding to the scale of the proteome3,4,5,6,7. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties8,9, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we describe an initial version of a proteome-scale map of human binary protein–protein interactions. Using a stringent, high-throughput yeast two-hybrid system, we tested pairwise interactions among the products of 8,100 currently available Gateway-cloned open reading frames and detected 2,800 interactions. This data set, called CCSB-HI1, has a verification rate of 78% as revealed by an independent co-affinity purification assay, and correlates significantly with other biological attributes. The CCSB-HI1 data set 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. This work represents an important step towards a systematic and comprehensive human interactome project.

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Figure 1: Towards the generation of a proteome-scale human yeast two-hybrid map.
Figure 2: Overlap of CCSB-HI1 with existing literature-curated (LC) data.
Figure 3: Interaction network of disease-associated CCSB-HI1 proteins.

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This paper is dedicated to the memory of Stan Korsmeyer. We thank members of the Vidal laboratory and the participants of the ORFeome Meeting for discussions; the sequencing staff at Agencourt Biosciences for technical assistance; E. Smith for his help with the figures; C. McCowan, A. Bird, T. Clingingsmith and C. You for administrative assistance; and E. Benz, S. Korsmeyer, D. Livingston, P. McCue, J. Song, B. Rollins and the DFCI Strategic Planning Initiative for support. Our human interactome project is supported by the DFCI High-Tech Fund (S. Korsmeyer), an Ellison Foundation grant awarded to M.V., an NIH/NCI grant awarded to S. Korsmeyer, S. Orkin, G. Gilliland and M.V., an ‘interactome mapping’ grant from NIH/NHGRI and NIH/NIGMS awarded to F.P.R. and M.V., and a W.M. Keck Foundation grant awarded to E. Benz, J. Marto, F.P.R. and M.V. Other support includes Taplin Funds for Discovery (F.P.R., F.D.G. and G.F.B), a 2003 NSF Fellowship (D.S.G) and funding from the Fonds National de la Recherche Scientifique, Belgium (M.D.). Author Contributions Experiments and data analyses were coordinated by J.F.R., T.H. and K.V. High-throughput ORF cloning and yeast two-hybrid screens were performed by J.F.R., T.H.K., A.D., N.L., N.A.G., J.R. and J.L. J.F.R developed the high-throughput yeast two-hybrid strategy. Computational analyses were performed by T.H., K.V., G.F.B., F.D.G., N.K., P.L., D.S.G., L.V.Z., S.L.W. and G.F. Co-affinity purification experiments were performed by M.D., C.S., J.F.R., S.M., M.B., S.L. and J.S.A. C.F., E.L., S.C. and C.B. provided laboratory support. R.S.S., J.V., H.Y.Z., A.S. and M.E.C. helped with the overall interpretation of the data. DNA sequencing was performed by S.B., R.S. and L.D.S. The manuscript was written by J.F.R., K.V., M.E.C., D.E.H., F.P.R. and M.V. The project was conceived by M.V. and co-directed by D.E.H., F.P.R. and M.V.

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Correspondence to David E. Hill, Frederick P. Roth or Marc Vidal.

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Supplementary information

Supplementary Data

This file contains expanded information regarding various concepts discussed in the main paper, plus a Methods section. In addition, this file has a Supplementary Methods section and legends for the Supplementary Figures and Tables. (DOC 518 kb)

Supplementary Figure S1a

Filtering and quality assessment of Y2H interactions. (PDF 451 kb)

Supplementary Figure S1b

Filtering and quality assessment of Y2H interactions. (PDF 33623 kb)

Supplementary Figure S1c

Filtering and quality assessment of Y2H interactions. (PDF 3236 kb)

Supplementary Figure S2

Bias in network neighborhoods for either CCSB-HI1 or LCI interactions. (PDF 225 kb)

Supplementary Figure S3

Occurrence of CCSB-HI1-associated, LCI-associated associated gene pairs in Pubmed or Google Scholar searches. (PDF 200 kb)

Supplementary Figure S4a

Correlation of interaction data with other gene- or protein-pair characteristics. (PDF 1646 kb)

Supplementary Figure S4b

Correlation of interaction data with other gene- or protein-pair characteristics. (PDF 233 kb)

Supplementary Figure S5a

Network analyses of CCSB-HI1. (PDF 181 kb)

Supplementary Figure S5b

Network analyses of CCSB-HI1. (PDF 182 kb)

Supplementary Figure S5c

Network analyses of CCSB-HI1. (PDF 247 kb)

Supplementary Figure S5d

Network analyses of CCSB-HI1. (PDF 108 kb)

Supplementary Figure S6a

Sub-networks of putative biological modules. (PDF 476 kb)

Supplementary Figure S6b

Sub-networks of putative biological modules. (PDF 262 kb)

Supplementary Figure S6c

Sub-networks of putative biological modules. (PDF 191 kb)

Supplementary Table S1

List of all human ORFs in Space-I that were tested for Y2H interactions. (XLS 226 kb)

Supplementary Table S2

List of CCSB-HI1 and LCI binary interactions along with annotation. (XLS 254 kb)

Supplementary Table S3

List of CCSB-HI1 and LCI interactions that were tested in co-AP experiments. (XLS 6 kb)

Supplementary Table S4

List of over-represented and under-represented Pfam-A domains in CCSB-HI1 and LCI data sets. (XLS 23 kb)

Supplementary Table S5

Analysis of overlap between CCSB-HI1 or LCI-interacting protein-pairs with other shared gene- or protein-pair characteristics. (XLS 43 kb)

Supplementary Table S6

Statistics of CCSB-HI1interactions between proteins in different evolutionary classes. (XLS 20 kb)

Supplementary Table S7

List of 172 MCODE-generated clusters from the CCSB-HI1 network and the combined CCSB-HI1/LCI and CCSB-HI1/LC networks. (XLS 197 kb)

Supplementary Table S8

Potentially novel associations of proteins with genetic disorders as revealed by the CCSB-HI1 interaction data set. (XLS 89 kb)

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Rual, JF., Venkatesan, K., Hao, T. et al. Towards a proteome-scale map of the human protein–protein interaction network. Nature 437, 1173–1178 (2005).

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