NetGrep: fast network schema searches in interactomes

被引：21
作者：
Banks, Eric [1 ,2 ]
Nabieva, Elena [1 ,2 ]
Peterson, Ryan [1 ]
Singh, Mona [1 ,2 ]
机构：
[1] Princeton Univ, Dept Comp Sci, Princeton, NJ 08540 USA
[2] Princeton Univ, Carl Icahn Lab, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA
来源：
GENOME BIOLOGY | 2008年 / 9卷 / 09期
基金：
美国国家科学基金会; 美国国家卫生研究院;
关键词：
D O I：
10.1186/gb-2008-9-9-r138
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
NetGrep (http://genomics.princeton.edu/singhlab/netgrep/) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of descriptions of proteins (for example, their molecular functions or putative domains) along with the desired topology and types of interactions among them. Schemas can thus describe domain-domain interactions, signaling and regulatory pathways, or more complex network patterns. NetGrep provides an advanced graphical interface for specifying schemas and fast algorithms for extracting their matches.
引用
收藏
页数：13
相关论文
共 58 条
[31]   Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps [J].
Nabieva, E ;
Jim, K ;
Agarwal, A ;
Chazelle, B ;
Singh, M .
BIOINFORMATICS, 2005, 21 :I302-I310
[32]  
*NETGREP, NETGREP US GUID
[33]   Statistical analysis of domains in interacting protein pairs [J].
Nye, TMW ;
Berzuini, C ;
Gilks, WR ;
Babu, MM ;
Teichmann, SA .
BIOINFORMATICS, 2005, 21 (07) :993-1001
[34]   A domain interaction map based on phylogenetic profiling [J].
Pagel, P ;
Wong, P ;
Frishman, D .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 344 (05) :1331-1346
[35]   Functional annotation of regulatory pathways [J].
Pandey, Jayesh ;
Koyutuerk, Mehmet ;
Kim, Yohan ;
Szpankowski, Wojciech ;
Subramaniam, Shankar ;
Grama, Ananth .
BIOINFORMATICS, 2007, 23 (13) :I377-I386
[36]   Assembly of cell regulatory systems through protein interaction domains [J].
Pawson, T ;
Nash, P .
SCIENCE, 2003, 300 (5618) :445-452
[37]   Alignment of metabolic pathways [J].
Pinter, RY ;
Rokhlenko, O ;
Yeger-Lotem, E ;
Ziv-Ukelson, M .
BIOINFORMATICS, 2005, 21 (16) :3401-3408
[38]   Global analysis of protein phosphorylation in yeast [J].
Ptacek, J ;
Devgan, G ;
Michaud, G ;
Zhu, H ;
Zhu, XW ;
Fasolo, J ;
Guo, H ;
Jona, G ;
Breitkreutz, A ;
Sopko, R ;
McCartney, RR ;
Schmidt, MC ;
Rachidi, N ;
Lee, SJ ;
Mah, AS ;
Meng, L ;
Stark, MJR ;
Stern, DF ;
De Virgilio, C ;
Tyers, M ;
Andrews, B ;
Gerstein, M ;
Schweitzer, B ;
Predki, PF ;
Snyder, M .
NATURE, 2005, 438 (7068) :679-684
[39]   Inferring protein domain interactions from databases of interacting proteins [J].
Riley, R ;
Lee, C ;
Sabatti, C ;
Eisenberg, D .
GENOME BIOLOGY, 2005, 6 (10)
[40]   MAVisto:: a tool for the exploration of network motifs [J].
Schreiber, F ;
Schwöbbermeyer, H .
BIOINFORMATICS, 2005, 21 (17) :3572-3574
123456