TRANSFAC^® Release 7.0 - Documentation

Gene: Contents

Initially designed to link TRANSFAC^® data to the TRRD and Compel (now: TRANSCompel^TM) databases, the GENE table (2397 entries) has gained more and more a central role, as it is not only jointly used by several of our own databases (in addition to TRANSCompel^TM: TRANSPATH^®, PathoDB^® and S/MARt DB^TM), but has been extended to one of the major link sources to other, external databases (EMBL, BRENDA, LocusLink, OMIM, RefSeq). As some of the regulated genes encode transcription factors themselves (which sometimes may even give rise to autoregulatory or feedback loops) there are not only links from gene to regulating factor (via site), but also from gene to encoded factors and vice versa. In addition to link all these databases the GENE table serves to list the transcription factor binding sites (and composite elements of TRANSCompel^TM) within a gene regulatory region, and thus showing them in a context. Further, the GENE table contains the promoter classification number as proposed by P. Bucher. The ID of GENE entries is identical to that used in the TRANSFAC^® SITE table, except that the consecutive number which characterizes individual sites is missing.

TRRD is maintainened at the Institute of Cytology and Genetics (Siberian Department of the Russian Academy of Sciences, Novosibirsk, Russia).

Fields

AC        Accession no.
XX
ID        Identifier
XX
DT        Date; author
XX
SD        Short description/name of the gene
XX
DE        Description: long name of the gene
XX
SY        Synonyms of gene name
XX
OS        Biological species
OC        Taxonomic classification
XX
CH        Chromosomal location
XX
BC        Bucher promoter classification
XX
RG        Where and under what conditions the gene is expressed
XX
BS        SITE positions and accession numbers; Binding FACTOR
XX
CE        Composite element positions and accession number
XX
FA        Encoded factor
XX
DR        Database references (TRRD, EMBL, EntrezGene, REFSEQ, 
          UniGene, OMIM,
DR        TRANSPATH®, TRANSPROTM, PathoDB®, SMARtDBTM, BKL, Ensembl, 
          Affymetrix, HGNC, MGI, RGD)
XX
RN        Reference no.
RX        MEDLINE ID
RA        Reference authors
RT        Reference title
RL        Reference data
XX
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