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Literature DB >> 12819152

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.

Harukazu Suzuki¹, Rintaro Saito, Mutsumi Kanamori, Chikatoshi Kai, Christian Schönbach, Takeshi Nagashima, Junko Hosaka, Yoshihide Hayashizaki.

Abstract

Here, we describe the development of a mammalian protein-protein interaction (PPI) database and of a PPI Viewer application to display protein interaction networks (http://fantom21.gsc.riken.go.jp/PPI/). In the database, we stored the mammalian PPIs identified through our PPI assays (internal PPIs), as well as those we extracted and processed (external PPIs) from publicly available data sources, the DIP and BIND databases and MEDLINE abstracts by using FACTS, a new functional inference and curation system. We integrated the internal and external PPIs into the PPI database, which is linked to the main FANTOM2 viewer. In addition, we incorporated into the PPI Viewer information regarding the luciferase reporter activity of internal PPIs and the data confidence of external PPIs; these data enable visualization and evaluation of the reliability of each interaction. Using the described system, we successfully identified several interactions of biological significance. Therefore, the PPI Viewer is a useful tool for exploring FANTOM2 clone-related protein interactions and their potential effects on signaling and cellular communication.

Entities: Species

Mesh：

Year: 2003 PMID： 12819152 PMCID： PMC403706 DOI： 10.1101/gr.956303

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

33 in total

1. BIND--The Biomolecular Interaction Network Database.

Authors: G D Bader; I Donaldson; C Wolting; B F Ouellette; T Pawson; C W Hogue
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

Review 2. Protein-protein interactions define specificity in signal transduction.

Authors: T Pawson; P Nash
Journal: Genes Dev Date: 2000-05-01 Impact factor: 11.361

3. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

Authors: P Uetz; L Giot; G Cagney; T A Mansfield; R S Judson; J R Knight; D Lockshon; V Narayan; M Srinivasan; P Pochart; A Qureshi-Emili; Y Li; B Godwin; D Conover; T Kalbfleisch; G Vijayadamodar; M Yang; M Johnston; S Fields; J M Rothberg
Journal: Nature Date: 2000-02-10 Impact factor: 49.962

4. Protein interaction mapping in C. elegans using proteins involved in vulval development.

Authors: A J Walhout; R Sordella; X Lu; J L Hartley; G F Temple; M A Brasch; N Thierry-Mieg; M Vidal
Journal: Science Date: 2000-01-07 Impact factor: 47.728

Review 5. Tumor necrosis factor receptor-associated factor (TRAF) 2 and its role in TNF signaling.

Authors: H Wajant; P Scheurich
Journal: Int J Biochem Cell Biol Date: 2001-01 Impact factor: 5.085

Review 6. Mechanisms of vesicle formation: insights from the COP system.

Authors: F Wieland; C Harter
Journal: Curr Opin Cell Biol Date: 1999-08 Impact factor: 8.382

7. Functional annotation of a full-length mouse cDNA collection.

Authors: J Kawai; A Shinagawa; K Shibata; M Yoshino; M Itoh; Y Ishii; T Arakawa; A Hara; Y Fukunishi; H Konno; J Adachi; S Fukuda; K Aizawa; M Izawa; K Nishi; H Kiyosawa; S Kondo; I Yamanaka; T Saito; Y Okazaki; T Gojobori; H Bono; T Kasukawa; R Saito; K Kadota; H Matsuda; M Ashburner; S Batalov; T Casavant; W Fleischmann; T Gaasterland; C Gissi; B King; H Kochiwa; P Kuehl; S Lewis; Y Matsuo; I Nikaido; G Pesole; J Quackenbush; L M Schriml; F Staubli; R Suzuki; M Tomita; L Wagner; T Washio; K Sakai; T Okido; M Furuno; H Aono; R Baldarelli; G Barsh; J Blake; D Boffelli; N Bojunga; P Carninci; M F de Bonaldo; M J Brownstein; C Bult; C Fletcher; M Fujita; M Gariboldi; S Gustincich; D Hill; M Hofmann; D A Hume; M Kamiya; N H Lee; P Lyons; L Marchionni; J Mashima; J Mazzarelli; P Mombaerts; P Nordone; B Ring; M Ringwald; I Rodriguez; N Sakamoto; H Sasaki; K Sato; C Schönbach; T Seya; Y Shibata; K F Storch; H Suzuki; K Toyo-oka; K H Wang; C Weitz; C Whittaker; L Wilming; A Wynshaw-Boris; K Yoshida; Y Hasegawa; H Kawaji; S Kohtsuki; Y Hayashizaki
Journal: Nature Date: 2001-02-08 Impact factor: 49.962

8. The sequence of the human genome.

Authors: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal: Science Date: 2001-02-16 Impact factor: 47.728

Review 9. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm.

Authors: A J Walhout; S J Boulton; M Vidal
Journal: Yeast Date: 2000-06-30 Impact factor: 3.239

10. The genome sequence of Drosophila melanogaster.

Authors: M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal: Science Date: 2000-03-24 Impact factor: 47.728

6 in total

1. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

Authors: Piero Carninci; Kazunori Waki; Toshiyuki Shiraki; Hideaki Konno; Kazuhiro Shibata; Masayoshi Itoh; Katsunori Aizawa; Takahiro Arakawa; Yoshiyuki Ishii; Daisuke Sasaki; Hidemasa Bono; Shinji Kondo; Yuichi Sugahara; Rintaro Saito; Naoki Osato; Shiro Fukuda; Kenjiro Sato; Akira Watahiki; Tomoko Hirozane-Kishikawa; Mari Nakamura; Yuko Shibata; Ayako Yasunishi; Noriko Kikuchi; Atsushi Yoshiki; Moriaki Kusakabe; Stefano Gustincich; Kirk Beisel; William Pavan; Vassilis Aidinis; Akira Nakagawara; William A Held; Hiroo Iwata; Tomohiro Kono; Hiromitsu Nakauchi; Paul Lyons; Christine Wells; David A Hume; Michela Fagiolini; Takao K Hensch; Michelle Brinkmeier; Sally Camper; Junji Hirota; Peter Mombaerts; Masami Muramatsu; Yasushi Okazaki; Jun Kawai; Yoshihide Hayashizaki
Journal: Genome Res Date: 2003-06 Impact factor: 9.043