max planck institut
informatik

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

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Dataset versions

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

Differences between versions 1.0 and 2.0:

• 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 missing Affymetrix mRNA assignment are now included.

miRNA binding site prediction sources

• PicTar
• miRanda
• miRbase
• TargetScan

Embedded Database

The DomainGraph plugin uses an embedded database by Apache Derby.
The database will be installed locally in the user's Cytoscape directory upon first usage. It contains the mapping from UniProt and Ensembl identifiers
to Pfam domains, the domain-domain interaction datasets, the Affymetrix Exon Array mapping data and additional information provided with the plugin.

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• Algorithms & Complexity
• Computer Vision and Machine Learning
• Internet Architecture
• Computer Graphics
• Databases and Information Systems
• Research Group Computational Biology
  • People
  • Former Research Groups
  • Software
    • DomainGraph
    • Documentation
    • Tutorial
    • Sample Data
    • Download
• Automation of Logic