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Table 1 Data Types and Sources accessible by current annotation modules.

From: FACT – a framework for the functional interpretation of high-throughput experiments

Data source, access method Data provider, data location Type of annotation used by FACT
Ensembl, Perl API access to local or remote database European Bioinformatics Institute and Wellcome Trust Sanger Institute (GB) [8], http://www.ensembl.org Ensembl ID, Gene Symbol, Gene Name, Chromosomal Location, Homologues Genes, Interpro Domains, RefSeq Accession Number, Affymetrix ID
euGenes, local database University of Indiana (USA) [10], ftp://iubio.bio.indiana.edu/eugenes/ euGene ID, Gene Symbol, Gene Name, GDB ID, OMIM ID, Genomic Localization, GeneOntology Terms, Protein Accession Numbers
Image Consortium, local database Lawrence Livermore National Laboratory (USA) [28], ftp://image.llnl.gov/image/imagene/ Clone Image ID
Biological Biochemical Image Database, HTTP parser and HTTP request National Institute of Aging, NIH (USA) [11], http://bbid.grc.nia.nih.gov/cgi-bin/pathwaysearch.pl Pathway Name and Image-link
GeneOntology, local database GeneOntology Consortium [2], http://www.geneontology.org/GO.current.annotations.shtml ID and Name of GO-Term (Biological Process, Molecular Function, Cellular Localization)
Cancer Genome Anatomy Project, local database National Cancer Institute, NIH (USA) [29], ftp://ftp1.nci.nih.gov/pub/CGAP Biocarta name, Biocarta short name, KEGG Pathway Name, KEGG Pathway ID, PFAM ID
LocusLink / EntrezGene, local database NCBI/NIH (USA) [30], ftp://ftp.ncbi.nih.gov/refseq/LocusLink / ftp://ftp.ncbi.nih.gov/gene A. LocusLink ID, Gene Symbol, Gene Name, Genomic Localization, GeneOntology Terms, OMIM ID B. Key references (PubMed links)
Mouse Genome Database, local database Jackson Laboratory (USA) [31], ftp://ftp.informatics.jax.org MGI ID / Gene Symbol
Internal CloneBase, local database Deutsches Krebsforschungs zentrum, Div. Molecular Genetics (D) General Information on available Clones
CpG, local database University of California Santa Cruz (USA), ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/cpgIsland.txt.gz Calculated relative CpG content of genomic region
STRING, local database EMBL (D) [12], http://string.embl.de (medium or better confidence) Protein interaction data (computed and imported from other databases)
Affymetrix CEL files Affymetrix Inc. / FACT, http://www.affymetrix.com Use of Affymetrix probe IDs
Reactome, local database and HTTP request European Bioinformatics Institute (GB) [3], http://www.reactome.org/download Pathway information