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GraphWeb is a public web server for graph-based analysis of biological networks that:
  • analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes;
  • integrates multiple diverse datasets into global networks;
  • incorporates multispecies data using gene orthology mapping;
  • filters nodes and edges based on dataset support, edge weight and node annotation;
  • detects gene modules from networks using a collection of algorithms;
  • interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs.
J. Reimand*, L. Tooming*, H. Peterson, P. Adler, J. Vilo: GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. (2008)
Nucl. Acids Res. 2008 36: W452-W459; doi:10.1093/nar/gkn230 [ PDF ]

Example inputs

Example file Species Date last updated Explanation
C.elegans protein interactions (IntAct) C.elegans 2009/09/06 IntAct protein-protein interaction network of the worm C.elegans, including >4700 interacions of >2900 proteins (http://www.ebi.ac.uk/intact/).
Cattle protein interactions (IntAct) B.taurus 2009/09/06 IntAct protein-protein interaction network of cattle, including >180 interactions of >130 proteins (http://www.ebi.ac.uk/intact/).
Fly protein interactions (IntAct) D.melanogaster 2009/09/06 IntAct protein-protein interaction network of the fly D.melanogaster, including >25000 interacions of >8300 proteins (http://www.ebi.ac.uk/intact/).
Human BioGRID protein interactions H.sapiens 2013/10/04 BioGRID protein-protein interaction dataset from September 2013
Human combined protein interactions H.sapiens 2007/12/31 This dataset combines three sources of human protein-protein interaction networks, including data from the databases HPRD and IntAct and the automatic literature mining study by Ramani et al 2005.
Human heterogeneous networks H.sapiens 2007/12/31 This dataset combines 4 heterogeneous networks. The first network contains human gene coexpression relations measured over several public cancer-related datasets. The second and third networks contain PPI data: the human protein interaction network (~18700 interactions) and a network of orthologous interactions of mouse, rat, fly and yeast (~6700 interactions) from IntAct. The fourth network contains transcription factors and their target genes from the Transfac database.
Human literature mining protein interactions (Ramani et al) H.sapiens 2005/06/17 Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of human interactome, Ramani et al 2005. The dataset is based on automatic analysis of Medline abstracts and contains a network of 31,609 interactions among 7,748 human proteins. The data is available from http://bioinformatics.icmb.utexas.edu/idserve/.
Human protein interactions (HPRD) H.sapiens 2007/12/31 HPRD protein-protein interaction network of human, including >3600 interacions of >9000 proteins (http://www.hprd.org/).
Human protein interactions (IntAct) H.sapiens 2009/09/06 IntAct protein-protein interaction network of H.sapiens, including >20000 interacions of >7500 proteins (http://www.ebi.ac.uk/intact/).
Human protein interactions + mouse orthologs (IntAct) H.sapiens/M.musculus 2009/09/06 IntAct protein-protein interaction network of human, combined with orthologous interactions of mouse, including >23000 interacions of >9600 proteins (http://www.ebi.ac.uk/intact/).
Mouse protein interactions (IntAct) M.musculus 2009/09/06 IntAct protein-protein interaction network of the mouse M.musculus, including >2700 interacions of >2100 proteins (http://www.ebi.ac.uk/intact/).
Networks example in GraphWeb publication H.sapiens 2007/12/31
Rat protein interactions (IntAct) R.norvegicus 2009/09/06 IntAct protein-protein interaction network of the rat R.norvegicus, including >800 interacions of >800 proteins (http://www.ebi.ac.uk/intact/).
Yeast epistatic network from knockout data S.cerevisiae 2009/09/08 This yeast dataset combines genome-scale networks from 5 types of data: Gene expression measurements from transcription factor (TF) knockout microarrays (Hu et al 2007, edges between TFs and differentially expressed genes, indirect regulatory events removed using epistatic relations), ChIP-chip data (Harbison et al 2004, edges between TFs and genes with bound promoters), predicted regulatory motifs (MacIsaac et al 2006, Erb et al 2006, edges between TFs and genes with motifs in promoters), and two protein-protein interaction datasets (Yu et al 2008, Collins et al 2007). MCL clustering of above networks reveals dense functional modules.
Yeast protein interactions (IntAct) S.cerevisiae 2009/09/06 IntAct protein-protein interaction network of the yeast S.cerevisiae, including >37000 interacions of >5400 proteins (http://www.ebi.ac.uk/intact/).
Yeast transcription regulation network S.cerevisiae 2007/12/31 An improved map of conserved regulatory sites for Saccharomyces cerevisiae, MacIsaac et al 2006. A network based on ChIP-chip binding, motif discovery and sequence conservation, including 8704 interactions with 117 regulators and their targets.



GraphWeb 2007-2008
Laur Tooming & Jüri Reimand & Jaak Vilo @ BIIT Group, Institute of Computer Science, University of Tartu.