Computing graphlet signatures of network nodes and motifs in cytoscape with GraphletCounter

Bioinformatics

Volumn 28, Issue 2, 2012, Pages 290-291

  Whelan, Christopher ^a   S̈nmez, Kemal ^a  

^a Oregon Health and Science University Department of Biomedical Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; HUMAN; METHODOLOGY; SYSTEMS BIOLOGY;

HUMANS; SOFTWARE; SYSTEMS BIOLOGY; USER-COMPUTER INTERFACE;

EID: 84856118125     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr637     Document Type: Article

References (9)

1. Kashtan,N. et al. (2004) Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics, 20, 1746-1758.
2. Mangan,S. et al. (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J. Mol. Biol., 334, 197-204.
3. Milenković,T. and Pržulj,N. (2008) Uncovering biological network function via graphlet degree signatures. Cancer Infor., 6, 257-273.
4. Milenković,T. et al. (2008) GraphCrunch: a tool for large network analyses. BMC Bioinformatics, 9, 70.
5. Milenković, T. et al. (2010) Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. J. R Soc. Interface, 7, 423-437.
6. Milo,R. et al. (2002) Network motifs: simple building blocks of complex networks. Science, 298, 824-827.
7. Pržulj,N. et al. (2004) Modeling interactome: scale-free or geometric? Bioinformatics, 20, 3508-3515.
8. Pržulj,N. (2007) Biological network comparison using graphlet degree distribution. Bioinformatics, 23, e177-e183.
9. Shannon,P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.