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GraphWeb specifications

Information


Unique identifier OMICS_16580
Name GraphWeb
Interface Web user interface
Restrictions to use None
Input data A combined biological network of a selected species, consisting of genes, proteins or microarray probesets as nodes and corresponding associations as edges.
Output data A table containing one row for each graph module found, with the following columns containing links to results: node name conversion, number of nodes, list nodes, list edges, zoom in, label distribution, score, g:Profiler annotations, visualisations.
Programming languages C++, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jaak Vilo <>

Publication for GraphWeb

GraphWeb in publications

 (9)
PMCID: 5810221
PMID: 29393370
DOI: 10.3892/ijmm.2018.3422

[…] were selected to construct a co-expression network, which was visualized using cytoscape2.8.0 (http://www.cytoscape.org/). functional modules in the co-expression network were identified using the graphweb tool (http://biit.cs.ut.ee/graphweb/) ()., the 152 gbm tumor samples from tcga were stratified into two groups based on good prognosis and bad prognosis. the good prognosis group […]

PMCID: 5810222
PMID: 29393333
DOI: 10.3892/ijmm.2018.3401

[…] were also searched using database for annotation, visualization and integrated discovery (david) software (david.ncifcrf.gov/) (). the functional clusters in the network were extracted using the graphweb tool (biit.cs.ut.ee/graphweb/) ()., to establish a prognostic prediction system, the expression data of the 272 samples with survival information in tcga dataset served as the training […]

PMCID: 5780129
PMID: 29115420
DOI: 10.3892/mmr.2017.7850

[…] genes were screened using the cox regression analysis in the survival package, and co-expression network and module analyses were performed separately using cytoscape software and graphweb tool, respectively. after a prognostic prediction system was constructed and validated, enrichment analysis of the signature genes was performed using the clusterprofiler package. a total […]

PMCID: 5706890
PMID: 29212244
DOI: 10.18632/oncotarget.21783

[…] the relationships between mirna-mediated cerna crosstalk and their functions, we performed a module analysis in the cerna network. we found six significant cerna modules (figure , ) based on graphweb. many genes and lncrnas competitively combined with mirnas in each module. for example, ddx24, bat2l1, adnp, gdi1, cep170, epb41l2, birc6 and d2hgdh competitively combined with mir-34a […]

PMCID: 5356814
PMID: 27911271
DOI: 10.18632/oncotarget.13683

[…] topological properties of the igsf genes were analyzed in both idnn and iddn., based on the iddn constructed by the igsf and breast cancer driver genes, we identified all the network modules using graphweb [], a web server for identifying the network-based biomarkers that best represent the property of the network. the graphweb web server was made of three component processes: (i) network […]


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GraphWeb institution(s)
University of Tartu, Institute of Computer Science, Tartu, Estonia; EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; University of Tartu, Institute of Molecular and Cell Biology, Tartu, Estonia; QureTec Ltd. Ulikooli, Tartu, Estonia
GraphWeb funding source(s)
This work has been supported by the EU FP6 grants ENFIN LSHG-CT-2005-518254 and COBRED LSHB-CT-2007-037730, Estonian Science Foundation grant ETF7437, and funding from the Marie Curie Biostar program and the Tiger University program of the Estonian Information Technology Foundation.

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