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 citations

 (2)
library_books

A 65 gene signature for prognostic prediction in colon adenocarcinoma

2018
PMCID: 5810222
PMID: 29393333
DOI: 10.3892/ijmm.2018.3401

[…] work 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/) (). […]

library_books

Protein Complex Discovery by Interaction Filtering from Protein Interaction Networks Using Mutual Rank Coexpression and Sequence Similarity

2015
Biomed Res Int
PMCID: 4322317
PMID: 25692131
DOI: 10.1155/2015/165186

[…] , the average coexpression, and the functional score—in the clusters before and after the addition of neighbouring proteins—were compared with one another. The functional score was calculated by the “GraphWeb” web server, using the g:Profiler data [, ]. Once a cluster has been identified by the MCL algorithm, the GraphWeb automatically assesses its biological importance through the known propertie […]

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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