DomainGraph

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Release 2.01, December 2008

System Requirements

The plugin works with Cytoscape 2.5 and 2.6, which requires Java SE 5 or Java SE 6.

Dataset Versions

Release 2.01 is based on UniProt version 14.1, Ensembl 49 and Pfam version 23.

Domain-Domain-Interaction Datasets:

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.)

miRNA annotation sources:

DomainGraph database versions:

In 1.0, the probeset-to-Ensembl-transcript mappings are taken from Affymetrix directly.
In 2.0, the mRNA assignment is done according to the genomic positions of the probesets. mRNAs previously missing due to exclusion in Affymetrix mRNA assignment are now included.

Download

Download DomainGraph Release 2.01.

Contributors

Dorothea Emig¹, Nathan Salomonis², Melissa S. Cline³, Jan Baumbach⁴, Thomas Lengauer¹, Mario Albrecht¹, Anne Kunert⁵, Karsten Klein⁵, Petra Mutzel⁵

¹ Department of Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
² The J. David Gladstone Institutes, San Francisco, CA, USA
³ Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
⁴ International Computer Science Institute, Berkeley, CA, USA
⁵ Dortmund University of Technology, Dortmund, Germany