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Methods: Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
- Haiyuan Yu,
- Nicholas M. Luscombe,
- Hao Xin Lu,
- Xiaowei Zhu,
- Yu Xia,
- Jing-Dong J. Han,
- Nicolas Bertin,
- Sambath Chung,
- Marc Vidal,
- and Mark Gerstein
Genome Res. June 2004 14: 1107-1118; doi:10.1101/gr.1774904
.... The results of the newly produced interaction maps and regulatory networks are stored in an interolog/regulog database. Future Directions There are several directions to extend this work. With respect to the conservation of protein–protein interactions, there are many more sequenced s without known -wide...
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RESOURCE: The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer
- Harukazu Suzuki,
- Rintaro Saito,
- Mutsumi Kanamori,
- Chikatoshi Kai,
- Christian Schönbach,
- Takeshi Nagashima,
- Junko Hosaka,
- and Yoshihide Hayashizaki
Genome Res. June 2003 13: 1534-1541; doi:10.1101/gr.956303
....R., Vaglio, P., Reboul, J., Ge, H., Davis, B.P., Garrels, J., Vincent, S., and Vidal, M. 2001 . Identification of potential interaction networks using sequence-based searches for conserved protein–protein interactions or “interologs”. Genome Res. 11 : 2120 -2126. ↵ Nagashima, T., Silva, D.G., Petrovsky, N...
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RECOMB Special/Review: Protein networks in disease
- Trey Ideker and
- Roded Sharan
Genome Res. April 2008 18: 644-652; doi:10.1101/gr.071852.107
...Bioinformatics (Suppl. 5) 7 : S19 , doi: 10.1186/1471-2105-7-S5-S19 . ↵ Matthews, L.R. , Vaglio, P. , Reboul, J. , Ge, H. , Davis, B.P. , Garrels, J. , Vincent, S. , Vidal, M. ( 2001 ) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions...
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Methods: Græmlin: General and robust alignment of multiple large interaction networks
- Jason Flannick,
- Antal Novak,
- Balaji S. Srinivasan,
- Harley H. McAdams,
- and Serafim Batzoglou
Genome Res. September 2006 16: 1169-1181; Published in Advance August 9, 2006, doi:10.1101/gr.5235706
...functional modules within a large database of microbial networks. Source code is also available under the GNU Public License. Methods Græmlin is a network alignment algorithm capable of searching large sets of dense interaction networks for evolutionarily conserved functional modules, which are groups...
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Methods: Systematic identification of functional orthologs based on protein network comparison
- Sourav Bandyopadhyay,
- Roded Sharan,
- and Trey Ideker
Genome Res. March 2006 16: 428-435; Published in Advance April 4, 2006, doi:10.1101/gr.4526006
...Res. 13 : 2178 –2189. ↵ Matthews, L.R., Vaglio, P., Reboul, J., Ge, H., Davis, B.P., Garrels, J., Vincent, S., and Vidal, M. 2001 . Identification of potential interaction networks using sequence-based searches for conserved protein–protein interactions or “interologs.” Genome Res. 11 : 2120 –2126...
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Resource: Global networks of functional coupling in eukaryotes from comprehensive data integration
- Andrey Alexeyenko and
- Erik L.L. Sonnhammer
Genome Res. June 2009 19: 1107-1116; Published in Advance February 25, 2009, doi:10.1101/gr.087528.108
...-species pathway conservation analysis provided further support to these observations. The high-throughput functional analysis of genes and proteins is producing vast data resources that, if integrated into interaction networks, will be key to unraveling the function of all genes in an organism ( Sonnhammer 2005...
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INSIGHT/OUTLOOK: Intraproteomic Networks: New Forays Into Predicting Interaction Partners
- L. Aravind and
- Lakshminarayan M. Iyer
Genome Res. August 1, 2002 12: 1156-1158; doi:10.1101/gr.353302
.... , Davis B.P. , Garrels J. , Vincent S. , Vidal M. ( 2001 ) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or interologs. Genome Res. 11 : 2120 – 2126 . ↵ O'Shea E.K. , Rutkowski R. , Kim P.S. ( 1989 ) Evidence that the leucine...
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Resource: Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network
- Gabriel Markson,
- Christina Kiel,
- Russell Hyde,
- Stephanie Brown,
- Panagoula Charalabous,
- Anja Bremm,
- Jennifer Semple,
- Jonathan Woodsmith,
- Simon Duley,
- Kourosh Salehi-Ashtiani,
- Marc Vidal,
- David Komander,
- Luis Serrano,
- Paul Lehner,
- and Christopher M. Sanderson
Genome Res. October 2009 19: 1905-1911; Published in Advance June 23, 2009, doi:10.1101/gr.093963.109
...interaction networks using sequence-based searches for conserved protein–protein interactions or ‘‘interologs.’’ Genome Res 11: 2120–2126. Ozkan E, Yu H, Deisenhofer J. 2005. Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases. Proc Natl Acad Sci...
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RESOURCE: A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands
- Cosmas Giallourakis,
- Zhifang Cao,
- Todd Green,
- Heather Wachtel,
- Xiaohui Xie,
- Marco Lopez-Illasaca,
- Mark Daly,
- John Rioux,
- and Ramnik Xavier
Genome Res. August 2006 16: 1056-1072 ; Published in Advance July 6, 2006, doi:10.1101/gr.5285206
...manual literature curation. Step (2): Analyzed characteristics of PDZ–ligand interaction network including expression correlation between PDZ-encoding gene and ligand gene sets, as well as properties of bona fide ligands (e.g., level of PDZ-binding motif conservation). Step (3): Identified that 96...
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PERSPECTIVE: Changing perspectives in yeast research nearly a decade after the genome sequence
- Kara Dolinski and
- David Botstein
Genome Res. December 2005 15: 1611-1619; doi:10.1101/gr.3727505
...transcriptional networks. In two independent comparative genomics studies, conserved regulatory elements were identified by aligning the intergenic regions of closely related Saccharomyces species and then searching within them for conserved sequence motifs ( Cliften et al. 2003 ; Kellis et al. 2003 ). Pritsker...

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