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：
美国国家卫生研究院; 美国国家科学基金会;
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.
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页数：13
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共 58 条
  • [1] Biomolecular network motif counting and discovery by color coding
    Alon, Noga
    Dao, Phuong
    Hajirasouliha, Iman
    Hormozdiari, Fereydoun
    Sahinalp, S. Cenk
    [J]. BIOINFORMATICS, 2008, 24 (13) : I241 - I249
  • [2] Gene Ontology: tool for the unification of biology
    Ashburner, M
    Ball, CA
    Blake, JA
    Botstein, D
    Butler, H
    Cherry, JM
    Davis, AP
    Dolinski, K
    Dwight, SS
    Eppig, JT
    Harris, MA
    Hill, DP
    Issel-Tarver, L
    Kasarskis, A
    Lewis, S
    Matese, JC
    Richardson, JE
    Ringwald, M
    Rubin, GM
    Sherlock, G
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [3] BANKS E, PLOS COMPUT IN PRESS
  • [4] Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI [10.1093/nar/gkr1065, 10.1093/nar/gkp985, 10.1093/nar/gkh121]
  • [5] Osprey: a network visualization system
    Breitkreutz, BJ
    Stark, C
    Tyers, M
    [J]. GENOME BIOLOGY, 2003, 4 (03)
  • [6] CHENG Q, 2007, P RECOMB SAT C SYST
  • [7] Inferring domain-domain interactions from protein-protein interactions
    Deng, MH
    Mehta, S
    Sun, FZ
    Chen, T
    [J]. GENOME RESEARCH, 2002, 12 (10) : 1540 - 1548
  • [8] Dost B, 2007, LECT NOTES COMPUT SC, V4453, P1
  • [9] NetMatch: a Cytoscape plugin for searching biological networks
    Ferro, A.
    Giugno, R.
    Pigola, G.
    Pulvirenti, A.
    Skripin, D.
    Bader, G. D.
    Shasha, D.
    [J]. BIOINFORMATICS, 2007, 23 (07) : 910 - 912
  • [10] Graemlin: General and robust alignment of multiple large interaction networks
    Flannick, Jason
    Novak, Antal
    Srinivasan, Balaji S.
    McAdams, Harley H.
    Batzoglou, Serafim
    [J]. GENOME RESEARCH, 2006, 16 (09) : 1169 - 1181
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