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DomainGraph specifications

Information


Unique identifier OMICS_04275
Name DomainGraph
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 3.01
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Maintainers


  • person_outline Nathan Salomonis <>
  • person_outline Dorothea Emig <>
  • person_outline DomainGraph Team <>

Publication for DomainGraph

DomainGraph in publications

 (4)
PMCID: 4320441
PMID: 25523101
DOI: 10.1186/1756-0500-7-934

[…] case of individual small-scale analysis, researchers generally check alterations of amino acid sequences and of functional protein domains according to usages of alternative exons. altanalyze and domaingraph could provide protein domain information from alternative exons although this type of analysis of exons has been rarely applied comprehensively []., previously, we analyzed […]

PMCID: 4204855
PMID: 25335079
DOI: 10.1371/journal.pone.0110134

[…] exon/intron/splicing annotation were assigned to these results. a splice index p-value cut-off of <0.05 was used to filter alternative exon results. altexonviewer – a component of altanalyze and domaingraph - a cytoscape plugin were used to visualize splice index values and alternatively spliced exons. the splicing index (si) value was calculated as described in . briefly, si is log2 ratio […]

PMCID: 3167639
PMID: 21646333
DOI: 10.1093/nar/gkr405

[…] had z scores>2, microrna binding sites had z scores >2 and had a benjamini-hochberg p < 0.05, were reported. the altanalyze export file for graphic presentation of domain architecture by domaingraph is provided as file s6 in supplementary data., the filtered as genes were subjected to gene ontology enrichment analysis using altanalyze bundled module go-elite […]

PMCID: 2572699
PMID: 18710874
DOI: 10.1093/bioinformatics/btn437

[…] allow for measuring gene expression at the exon level and thus for studying alternative transcripts and their corresponding protein domain architecture. we have developed the cytoscape plugin domaingraph that enables the visualization and detailed study of domain–domain interactions forming protein interaction networks. in addition, the integration of exon expression data supports […]


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DomainGraph institution(s)
Max Planck Institute for Informatics, Saarbrucken, Germany; International Computer Science Institute, University of California, Berkeley, CA, USA; Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA; Department of Medicine and Department of Molecular and Cellular Pharmacology, University of California, San Francisco, CA, USA
DomainGraph funding source(s)
Supported by Boehringer Ingelheim Fonds; German National Genome Research Network (NGFN; 01GS0817; German Research Foundation (DFG; KFO 129/ 1-2); National Institutes of Health (NIH; GM080223, HG003053, HL66621).

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