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Constructing a Domain Graph

Contents

  1. Dataset Versions
  2. Constructing a Domain Graph
  3. Integration of Expression Data for Single Experiments
  4. Integration of AltAnalyze Data
  5. Preprocessing of Affymetrix Data
  6. Analysis
  7. Options

Interaction networks

The user has to import a gene or protein interaction network of interest. For the gene interaction networks, all encoded proteins and their domain compositions
will be shown. Protein interaction networks will be decomposed into the underlying domain-domain interactions by the plugin.
The user can either choose an interaction network that was preloaded into Cytoscape or import a new interaction network via the DomainGraph menu.

File Format:      All file formats supported by Cytoscape can be imported into the DomainGraph plugin.
Supported gene identifiers:
  • Ensembl Gene ID (e.g. ENSG00000188681)
  • Entrez Gene ID (e.g. 6310)
Supported protein identifiers:
  • UniProt Accession Number (e.g. P29466)
  • Ensembl Transcript ID (e.g. ENST00000260309)
  • Ensembl Peptide ID (e.g. ENSP00000260309)
Supported species:
  • Homo sapiens
  • Saccharomyces cerevisiae
  • Drosophila melanogaster
  • Caenorhabditis elegans
  • Mus musculus
  • Rattus norvegicus
  • Arabidopsis thaliana
  • Escherichia coli
  • Schizosaccharomyces pombe
  • Plasmodium falciparum
  • Danio rerio
  • Gallus gallus

Domain-domain interactions

DomainGraph provides several datasets, from which the domain-domain interaction network can be constructed. Structural datasets contain domain-domain
interactions that are derived from PDB structures, and predicted domain-domain interactions are obtained via computational methods.
To obtain additional information on the datasets, please follow the dataset links to their sources.

Structural datasets:
  • iPfam version 21
  • 3did version of November 2007
Predicted datasets:
  • InterDom version 2.0
  • LLZ
  • DPEA
  • DIMA version 2.0, consisting of 3 subsets (domain profiling, DPEA, and string)
  • LDSC consisting of 2 sets: all interactions and a core subset
  • RDFF
  • RCDP50
  • APMM consisting of 2 sets: APMM1 and APMM2
  • LP
  • PINS
  • IPPRI (Schelhorn, S.E., Lengauer, T., Albrecht, M. (2008) An integrative approach for predicting interactions of protein regions. Bioinformatics, in press.)

Domain graph views

For a domain graph, you can choose one of two different views for gene networks and three different views for protein networks (and you can switch between them any time):

Extended view (Gene network): Every gene is shown together with all its proteins and their contained Pfam domains.
Gene network view: You start with the gene network only.
Extended view (Protein network): Every protein is shown together with all its contained Pfam domains.
Compact view (Protein network): Each Pfam domain is shown only once and all proteins containing the domain are linked to this domain node.
Protein network view:      You start with the protein network without showing any domains. You can then individually select proteins, for which
you want to see the domain composition and the domain interactions.

Additional Features

The plugin provides additional information on the genes, proteins and respective domains via tooltips and a graphical representation of the protein composition.

You can see an example of the additional information here.