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 |