Web-based network analysis and visualization using CellMaps

Bioinformatics

Volumn 32, Issue 19, 2016, Pages 3041-3043

  Salavert, Francisco ^a,b   García Alonso, Luz ^a   Sánchez, Rubén ^a   Alonso, Roberto ^a   Bleda, Marta ^c   Medina, Ignacio ^d   Dopazo, Joaquín ^a,b,e  

^a CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^b CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e INSTITUTO DE SALUD CARLOS III   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; INTERNET; SOFTWARE;

BIOCHEMICAL PHENOMENA; INTERNET; SOFTWARE;

EID: 84990985632     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw332     Document Type: Article

References (16)

1. Al-Shahrour, F. et al. (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20, 578-580.
2. Alonso, R. et al. (2015) Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic Acids Res., 43, W117-W121.
3. Amadoz, A. et al. (2015) Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity. Sci. Rep., 5, 18494.
4. Bleda, M. et al. (2012a) Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res., 40, W168-W172.
5. Bleda, M. et al. (2012b) CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res., 40, W609-W614.
6. Csardi, G. and Nepusz, T. (2006) The igraph software package for complex network research. Int. J. Complex Syst., 1695. http://igraph.org/c/doc/ igraph-introduction.html#idm470952874400.
7. Franceschini, A. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-D815.
8. Franz, M. et al. (2015) Cytoscape.js: a graph theory library for visualisation and analysis. Bioinformatics. 32, 309-311.
9. Garcia-Alonso, L. et al. (2012) Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res, 40, e158.
10. Hu, Z. et al. (2013) VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res., 41, W225-W231.
11. Minguez, P. et al. (2009) SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res., 37, W109-W114.
12. Porta-Pardo, E. et al. (2015) A pan-cancer catalogue of cancer driver protein interaction interfaces. PLoS Comput. Biol., 11, e1004518.
13. Pratt, D. et al. (2015) NDEx: the network data exchange. Cell Syst., 1, 302-305.
14. Sebastian-Leon, P. et al. (2013) Inferring the functional effect of gene expression changes in signaling pathways. Nucleic Acids Res., 41, W213-W217.
15. Taubert, J. et al. (2014) Ondex Web: web-based visualization and exploration of heterogeneous biological networks. Bioinformatics, 30, 1034-1035.
16. Warde-Farley, D. et al. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res., 38, W214-W220.