SPIKE: a database of highly curated human signaling pathways

被引：55

作者：

Paz, Arnon ^{[3
]}

Brownstein, Zippora ^{[3
]}

Ber, Yaara ^{[2
]}

Bialik, Shani ^{[2
]}

David, Eyal ^{[3
]}

Sagir, Dorit ^{[3
]}

Ulitsky, Igor ^{[1
]}

Elkon, Ran ^{[3
]}

Kimchi, Adi ^{[2
]}

Avraham, Karen B. ^{[3
]}

Shiloh, Yosef ^{[3
]}

Shamir, Ron ^{[1
]}

机构：

[1] Tel Aviv Univ, Blavatnik Sch Comp Sci, IL-69978 Tel Aviv, Israel

[2] Weizmann Inst Sci, Dept Mol Genet, IL-76100 Rehovot, Israel

[3] Tel Aviv Univ, Sackler Sch Med, Dept Human Mol Genet & Biochem, IL-69978 Tel Aviv, Israel

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

以色列科学基金会;

关键词：

PROTEIN INTERACTION NETWORK; REPRESENTATION;

D O I：

10.1093/nar/gkq1167

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The rapid accumulation of knowledge on biological signaling pathways and their regulatory mechanisms has highlighted the need for specific repositories that can store, organize and allow retrieval of pathway information in a way that will be useful for the research community. SPIKE (Signaling Pathways Integrated Knowledge Engine; http://www.cs.tau.ac.il/similar to spike/is a database for achieving this goal, containing highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction. To make database population and pathway comprehension straightforward, a simple yet informative data model is used, and pathways are laid out as maps that reflect the curator's understanding and make the utilization of the pathways easy. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. The database is accompanied by a stand-alone software tool for analysis and dynamic visualization of pathways.

引用

页码：D793 / D799

页数：7

共 20 条

[1] The IntAct molecular interaction database in 2010 [J].

Aranda, B. ;

Achuthan, P. ;

Alam-Faruque, Y. ;

Armean, I. ;

Bridge, A. ;

Derow, C. ;

Feuermann, M. ;

Ghanbarian, A. T. ;

Kerrien, S. ;

Khadake, J. ;

Kerssemakers, J. ;

Leroy, C. ;

Menden, M. ;

Michaut, M. ;

Montecchi-Palazzi, L. ;

Neuhauser, S. N. ;

Orchard, S. ;

Perreau, V. ;

Roechert, B. ;

van Eijk, K. ;

Hermjakob, H. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D525-D531

[2] A large-scale RNAi screen in human cells identifies new components of the p53 pathway [J].

Berns, K ;

Hijmans, EM ;

Mullenders, J ;

Brummelkamp, TR ;

Velds, A ;

Heimerikx, M ;

Kerkhoven, RM ;

Madiredjo, M ;

Nijkamp, W ;

Weigelt, B ;

Agami, R ;

Ge, W ;

Cavet, G ;

Linsley, PS ;

Beijersbergen, RL ;

Bernards, R .

NATURE, 2004, 428 (6981) :431-437

[3]

Braun P, 2009, NAT METHODS, V6, P91, DOI [10.1038/NMETH.1281, 10.1038/nmeth.1281]

[4] MINT, the molecular interaction database: 2009 update [J].

Ceol, Arnaud ;

Aryamontri, Andrew Chatr ;

Licata, Luana ;

Peluso, Daniele ;

Briganti, Leonardo ;

Perfetto, Livia ;

Castagnoli, Luisa ;

Cesareni, Gianni .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D532-D539

[5] Chemical Entities of Biological Interest: an update [J].

de Matos, Paula ;

Alcantara, Rafael ;

Dekker, Adriano ;

Ennis, Marcus ;

Hastings, Janna ;

Haug, Kenneth ;

Spiteri, Inmaculada ;

Turner, Steve ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D249-D254

[6] The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

[7] SPIKE - a database, visualization and analysis tool of cellular signaling pathways [J].

Elkon, Ran ;

Vesterman, Rita ;

Amit, Nira ;

Ulitsky, Igor ;

Zohar, Idan ;

Weisz, Mali ;

Mass, Gilad ;

Orlev, Nir ;

Sternberg, Giora ;

Blekhman, Ran ;

Assa, Jackie ;

Shiloh, Yosef ;

Shamir, Ron .

BMC BIOINFORMATICS, 2008, 9 (1)

[8] Knowledge representation of signal transduction pathways [J].

Fukuda, K ;

Takagi, T .

BIOINFORMATICS, 2001, 17 (09) :829-837

[9] Transcriptional regulatory code of a eukaryotic genome [J].

Harbison, CT ;

Gordon, DB ;

Lee, TI ;

Rinaldi, NJ ;

Macisaac, KD ;

Danford, TW ;

Hannett, NM ;

Tagne, JB ;

Reynolds, DB ;

Yoo, J ;

Jennings, EG ;

Zeitlinger, J ;

Pokholok, DK ;

Kellis, M ;

Rolfe, PA ;

Takusagawa, KT ;

Lander, ES ;

Gifford, DK ;

Fraenkel, E ;

Young, RA .

NATURE, 2004, 431 (7004) :99-104

[10] ConsensusPathDB-a database for integrating human functional interaction networks [J].

Kamburov, Atanas ;

Wierling, Christoph ;

Lehrach, Hans ;

Herwig, Ralf .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D623-D628

← 1 2 →