Technical Details

Here you can find information for the database information which is used at the moment by BioProfiling.de tools.

Automatic Mapping

NCBI ftp site

Ftp Site File Downloading Date
ftp://ftp.ncbi.nih.gov/gene/DATA/ gene_info.gz 19.11.2010
ftp://ftp.ncbi.nih.gov/gene/DATA/ gene2refseq.gz 19.11.2010
ftp://ftp.ncbi.nih.gov/gene/DATA/ gene_refseq_uniprotkb_collab.gz 19.11.2010
ftp://ftp.ncbi.nih.gov/gene/DATA/ gene2unigene 19.11.2010
ftp://ftp.ncbi.nih.gov/gene/DATA/ gene2ensembl.gz 19.11.2010

EBI ftp site

Ftp Site File Downloading Date
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ ipi.HUMAN.dat.gz 19.11.2010
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ ipi.MOUSE.dat.gz 19.11.2010
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ ipi.RAT.dat.gz 19.11.2010
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ ipi.ARATH.dat.gz 19.11.2010

Affymetrix File

  • ATH1-121501.na29.annot.csv
  • Celegans.na29.annot.csv
  • DrosGenome1.na29.annot.csv
  • Drosophila_2.na29.annot.csv
  • HG-Focus.na29.annot.csv
  • HG-U133A.na29.annot.csv
  • HG-U133A_2.na29.annot.csv
  • HG-U219.na29.annot.csv
  • HT_HG-U133_Plus_PM.na29.annot.csv
  • HT_HG-U133A.na29.annot.csv
  • HT_HG-U133B.na29.annot.csv
  • HT_MG-430_PM.na29.annot.csv
  • HT_MG-430A.na29.annot.csv
  • HT_MG-430B.na29.annot.csv
  • Mouse430_2.na29.annot.csv
  • Mouse430A_2.na29.annot.csv
  • RAE230A.na29.annot.csv
  • RAE230B.na29.annot.csv
  • Rat230_2.na29.annot.csv
  • RatToxFX.na29.annot.csv

    • Tools

    ProfCom_GO

    Ftp Site File Downloading Date
    ftp://ftp.ncbi.nih.gov/gene/DATA/ gene2go.gz 19.11.2010

    ProfCom_INTERPRO

    Ftp Site File Downloading Date
    ftp://ftp.ebi.ac.uk/pub/databases/interpro/ protein2ipr.dat.gz 26.03.2011

    R spider

  • Human protein-protein interaction pairs, web site: http://www.reactome.org/download/, download date 19.11.2010
  • Arabidopsis thaliana protein-protein interaction pairs, web site: http://www.reactome.org/download/, download date 19.11.2010
  • Caenorhabditis elegans protein-protein interaction pairs, web site: http://www.reactome.org/download/, download date 19.11.2010
  • Mus musculus protein-protein interaction pairs, web site: http://www.reactome.org/download/, download date 19.11.2010
  • Rattus norvegicus protein-protein interaction pairs, web site: http://www.reactome.org/download/, download date 19.11.2010
  • Drosophila melanogaster protein-protein interaction pairs, web site: http://www.reactome.org/download/, download date 19.11.2010

    • PPI spider

  • file:all.zip, ftp site: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/, download date 19.11.2010

    • KEGG spider

  • file: KO, ftp site: ftp://ftp.genome.jp/pub/kegg/genes/, download date 19.11.2010
  • file: reaction, ftp site: ftp://ftp.genome.jp/pub/kegg/genes/, download date 19.11.2010
  • file: compound, ftp site: ftp://ftp.genome.jp/pub/kegg/genes/, download date 19.11.2010