Patikaweb:: a Web interface for analyzing biological pathways through advanced querying and visualization

被引：33

作者：

Dogrusoz, U ^{[1
]}

Erson, EZ ^{[1
]}

Giral, E ^{[1
]}

Demir, E ^{[1
]}

Babur, O ^{[1
]}

Cetintas, A ^{[1
]}

Colak, R ^{[1
]}

机构：

[1] Bilkent Univ, BCBI, TR-06800 Ankara, Turkey

来源：

BIOINFORMATICS | 2006年 / 22卷 / 03期

关键词：

D O I：

10.1093/bioinformatics/bti776

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

引用

页码：374 / 375

页数：2

共 8 条

[1] The universal protein resource (UniProt) [J].

Bairoch, A ;

Apweiler, R ;

Wu, CH ;

Barker, WC ;

Boeckmann, B ;

Ferro, S ;

Gasteiger, E ;

Huang, HZ ;

Lopez, R ;

Magrane, M ;

Martin, MJ ;

Natale, DA ;

O'Donovan, C ;

Redaschi, N ;

Yeh, LSL .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D154-D159

[2]

*BIOPAX, 2003, BIOL PATHW EXCH

[3] An ontology for collaborative construction and analysis of cellular pathways [J].

Demir, E ;

Babur, O ;

Dogrusoz, U ;

Gursoy, A ;

Ayaz, A ;

Gulesir, G ;

Nisanci, G ;

Cetin-Atalay, R .

BIOINFORMATICS, 2004, 20 (03) :349-356

[4]

Dogrusoz U, 2004, LECT NOTES COMPUT SC, V3383, P442

[5] The Gene Ontology (GO) database and informatics resource [J].

Harris, MA ;

Clark, J ;

Ireland, A ;

Lomax, J ;

Ashburner, M ;

Foulger, R ;

Eilbeck, K ;

Lewis, S ;

Marshall, B ;

Mungall, C ;

Richter, J ;

Rubin, GM ;

Blake, JA ;

Bult, C ;

Dolan, M ;

Drabkin, H ;

Eppig, JT ;

Hill, DP ;

Ni, L ;

Ringwald, M ;

Balakrishnan, R ;

Cherry, JM ;

Christie, KR ;

Costanzo, MC ;

Dwight, SS ;

Engel, S ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, RS ;

Sethuraman, A ;

Theesfeld, CL ;

Botstein, D ;

Dolinski, K ;

Feierbach, B ;

Berardini, T ;

Mundodi, S ;

Rhee, SY ;

Apweiler, R ;

Barrell, D ;

Camon, E ;

Dimmer, E ;

Lee, V ;

Chisholm, R ;

Gaudet, P ;

Kibbe, W ;

Kishore, R ;

Schwarz, EM ;

Sternberg, P ;

Gwinn, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261

[6] The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models [J].

Hucka, M ;

Finney, A ;

Sauro, HM ;

Bolouri, H ;

Doyle, JC ;

Kitano, H ;

Arkin, AP ;

Bornstein, BJ ;

Bray, D ;

Cornish-Bowden, A ;

Cuellar, AA ;

Dronov, S ;

Gilles, ED ;

Ginkel, M ;

Gor, V ;

Goryanin, II ;

Hedley, WJ ;

Hodgman, TC ;

Hofmeyr, JH ;

Hunter, PJ ;

Juty, NS ;

Kasberger, JL ;

Kremling, A ;

Kummer, U ;

Le Novère, N ;

Loew, LM ;

Lucio, D ;

Mendes, P ;

Minch, E ;

Mjolsness, ED ;

Nakayama, Y ;

Nelson, MR ;

Nielsen, PF ;

Sakurada, T ;

Schaff, JC ;

Shapiro, BE ;

Shimizu, TS ;

Spence, HD ;

Stelling, J ;

Takahashi, K ;

Tomita, M ;

Wagner, J ;

Wang, J .

BIOINFORMATICS, 2003, 19 (04) :524-531

[7] Reactome: a knowledgebase of biological pathways [J].

Joshi-Tope, G ;

Gillespie, M ;

Vastrik, I ;

D'Eustachio, P ;

Schmidt, E ;

de Bono, B ;

Jassal, B ;

Gopinath, GR ;

Wu, GR ;

Matthews, L ;

Lewis, S ;

Birney, E ;

Stein, L .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D428-D432

[8] Entrez Gene: gene-centered information at NCBI [J].

Maglott, D ;

Ostell, J ;

Pruitt, KD ;

Tatusova, T .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D54-D58

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