Genome Research International Con Genetics

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Matthews, L. R.
Right arrow Articles by Vidal, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Matthews, L. R.
Right arrow Articles by Vidal, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 11, Issue 12, 2120-2126, December 2001

METHODS
Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or "Interologs"

Lisa R. Matthews,1,2,3 Philippe Vaglio,1,3 Jérôme Reboul,1,3 Hui Ge,1 Brian P. Davis,2 James Garrels,2 Sylvie Vincent,1 and Marc Vidal1,4

Protein interaction maps have provided insight into the relationships among the predicted proteins of model organisms for which a genome sequence is available. These maps have been useful in generating potential interaction networks, which have confirmed the existence of known complexes and pathways and have suggested the existence of new complexes and or crosstalk between previously unlinked pathways. However, the generation of such maps is costly and labor intensive. Here, we investigate the extent to which a protein interaction map generated in one species can be used to predict interactions in another species.

Present address: 1Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston 02115, Massachusetts, USA; 2Proteome Inc., Beverly 01915, Massachusetts, USA.

3 These authors contributed equally to this work.

4 Corresponding author.

11:2120-2126 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
M. Michaut, S. Kerrien, L. Montecchi-Palazzi, F. Chauvat, C. Cassier-Chauvat, J.-C. Aude, P. Legrain, and H. Hermjakob
InteroPORC: automated inference of highly conserved protein interaction networks
Bioinformatics, July 15, 2008; 24(14): 1625 - 1631.
[Abstract] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
A. G. Pisabarro, G. Perez, J. L. Lavin, and L. Ramirez
Genetic networks for the functional study of genomes
Brief Funct Genomic Proteomic, June 25, 2008; (2008) eln026v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
D. Li, W. Liu, Z. Liu, J. Wang, Q. Liu, Y. Zhu, and F. He
PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources
Mol. Cell. Proteomics, June 1, 2008; 7(6): 1043 - 1052.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
B. Lehner and I. Lee
Network-guided genetic screening: building, testing and using gene networks to predict gene function
Brief Funct Genomic Proteomic, May 1, 2008; 7(3): 217 - 227.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
T. Ideker and R. Sharan
Protein networks in disease
Genome Res., April 1, 2008; 18(4): 644 - 652.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Cui, P. Li, G. Li, F. Xu, C. Zhao, Y. Li, Z. Yang, G. Wang, Q. Yu, Y. Li, et al.
AtPID: Arabidopsis thaliana protein interactome database an integrative platform for plant systems biology
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D999 - D1008.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Tarailo, S. Tarailo, and A. M. Rose
Synthetic Lethal Interactions Identify Phenotypic "Interologs" of the Spindle Assembly Checkpoint Components
Genetics, December 1, 2007; 177(4): 2525 - 2530.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y.-C. Chen, Y.-S. Lo, W.-C. Hsu, and J.-M. Yang
3D-partner: a web server to infer interacting partners and binding models
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W561 - W567.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Dutkowski and J. Tiuryn
Identification of functional modules from conserved ancestral protein protein interactions
Bioinformatics, July 1, 2007; 23(13): i149 - i158.
[Abstract] [Full Text] [PDF]

Home page
 J. Exp. Biol.Home page
B. Lehner
Modelling genotype-phenotype relationships and human disease with genetic interaction networks
J. Exp. Biol., May 1, 2007; 210(9): 1559 - 1566.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. A. Calderwood, K. Venkatesan, L. Xing, M. R. Chase, A. Vazquez, A. M. Holthaus, A. E. Ewence, N. Li, T. Hirozane-Kishikawa, D. E. Hill, et al.
Epstein-Barr virus and virus human protein interaction maps
PNAS, May 1, 2007; 104(18): 7606 - 7611.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. J. Cockell, B. Oliva, and R. M. Jackson
Structure-based evaluation of in silico predictions of protein protein interactions using Comparative Docking
Bioinformatics, March 1, 2007; 23(5): 573 - 581.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Hirsh and R. Sharan
Identification of conserved protein complexes based on a model of protein network evolution
Bioinformatics, January 15, 2007; 23(2): e170 - e176.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. F. Jonsson and P. A. Bates
Global topological features of cancer proteins in the human interactome
Bioinformatics, September 15, 2006; 22(18): 2291 - 2297.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. Flannick, A. Novak, B. S. Srinivasan, H. H. McAdams, and S. Batzoglou
Graemlin: General and robust alignment of multiple large interaction networks
Genome Res., September 1, 2006; 16(9): 1169 - 1181.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Chen, W. Hsu, M. L. Lee, and S.-K. Ng
Increasing confidence of protein interactomes using network topological metrics
Bioinformatics, August 15, 2006; 22(16): 1998 - 2004.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Guo, R. Liu, C. D. Shriver, H. Hu, and M. N. Liebman
Assessing semantic similarity measures for the characterization of human regulatory pathways
Bioinformatics, April 15, 2006; 22(8): 967 - 973.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
S. Bandyopadhyay, R. Sharan, and T. Ideker
Systematic identification of functional orthologs based on protein network comparison
Genome Res., March 1, 2006; 16(3): 428 - 435.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Wachi, K. Yoneda, and R. Wu
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
Bioinformatics, December 1, 2005; 21(23): 4205 - 4208.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
M. E. Cusick, N. Klitgord, M. Vidal, and D. E. Hill
Interactome: gateway into systems biology
Hum. Mol. Genet., October 15, 2005; 14(suppl_2): R171 - R181.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Espadaler, O. Romero-Isart, R. M. Jackson, and B. Oliva
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
Bioinformatics, August 15, 2005; 21(16): 3360 - 3368.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. McDermott, R. Bumgarner, and R. Samudrala
Functional annotation from predicted protein interaction networks
Bioinformatics, August 1, 2005; 21(15): 3217 - 3226.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Espadaler, R. Aragues, N. Eswar, M. A. Marti-Renom, E. Querol, F. X. Aviles, A. Sali, and B. Oliva
Detecting remotely related proteins by their interactions and sequence similarity
PNAS, May 17, 2005; 102(20): 7151 - 7156.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. R. Brown and I. Jurisica
Online Predicted Human Interaction Database
Bioinformatics, May 1, 2005; 21(9): 2076 - 2082.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Regul. Integr. Comp. Physiol.Home page
J. L. Renfro
Cell volume regulation: skating through the pathways
Am J Physiol Regulatory Integrative Comp Physiol, April 1, 2005; 288(4): R798 - R798.
[Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Sharan, S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R. M. Karp, and T. Ideker
From the Cover: Conserved patterns of protein interaction in multiple species
PNAS, February 8, 2005; 102(6): 1974 - 1979.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. Rev.Home page
P. Syntichaki and N. Tavernarakis
Genetic Models of Mechanotransduction: The Nematode Caenorhabditis elegans
Physiol Rev, October 1, 2004; 84(4): 1097 - 1153.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
D. E. Hill, M. A. Brasch, A. A. del Campo, L. Doucette-Stamm, J. I. Garrels, J. Glaven, J. L. Hartley, J. R. Hudson Jr., T. Moore, and M. Vidal
Academia-Industry Collaboration: An Integral Element for Building "Omic" Resources
Genome Res., October 1, 2004; 14(10b): 2010 - 2014.
[Full Text] [PDF]

Home page
 Genome Res.Home page
H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J.-D. J. Han, N. Bertin, S. Chung, M. Vidal, and M. Gerstein
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs
Genome Res., June 1, 2004; 14(6): 1107 - 1118.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. A. Malek, J. M. Wierzbowski, W. Tao, S. A. Bosak, D. J. Saranga, L. Doucette-Stamm, D. R. Smith, P. J. McEwan, and K. J. McKernan
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica
Nucleic Acids Res., February 10, 2004; 32(3): 1059 - 1064.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
S. Li, C. M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.-O. Vidalain, J.-D. J. Han, A. Chesneau, T. Hao, et al.
A Map of the Interactome Network of the Metazoan C. elegans
Science, January 23, 2004; 303(5657): 540 - 543.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. P. Kelley, R. Sharan, R. M. Karp, T. Sittler, D. E. Root, B. R. Stockwell, and T. Ideker
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
PNAS, September 30, 2003; 100(20): 11394 - 11399.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
H. Suzuki, R. Saito, M. Kanamori, C. Kai, C. Schonbach, T. Nagashima, J. Hosaka, and Y. Hayashizaki
The Mammalian Protein-Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer
Genome Res., June 1, 2003; 13(6): 1534 - 1541.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. Cooper, J. D. Clarke, P. Budworth, J. Kreps, D. Hutchison, S. Park, S. Guimil, M. Dunn, P. Luginbuhl, C. Ellero, et al.
A network of rice genes associated with stress response and seed development
PNAS, April 15, 2003; 100(8): 4945 - 4950.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
L. Aravind and L. M. Iyer
Intraproteomic Networks: New Forays Into Predicting Interaction Partners
Genome Res., August 1, 2002; 12(8): 1156 - 1158.
[Full Text] [PDF]

Home page
 Genome Res.Home page
S. Bandyopadhyay, R. Sharan, and T. Ideker
Systematic identification of functional orthologs based on protein network comparison
Genome Res., March 1, 2006; 16(3): 428 - 435.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.