TRANSFAC® Release 7.0 - Documentation
Initially designed to link TRANSFAC® data to the TRRD and Compel (now: TRANSCompelTM) 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 TRANSCompelTM: TRANSPATH®, PathoDB® and S/MARt DBTM),
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 TRANSCompelTM) 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).
AC Accession no.
DT Date; author
SD Short description/name of the gene
DE Description: long name of the gene
SY Synonyms of gene name
OS Biological species
OC Taxonomic classification
CH Chromosomal location
BC Bucher promoter classification
RG Where and under what conditions the gene is expressed
BS SITE positions and accession numbers; Binding FACTOR
CE Composite element positions and accession number
FA Encoded factor
DR Database references (TRRD, EMBL, EntrezGene, REFSEQ,
DR TRANSPATH®, TRANSPROTM, PathoDB®, SMARtDBTM, BKL, Ensembl,
Affymetrix, HGNC, MGI, RGD)
RN Reference no.
RX MEDLINE ID
RA Reference authors
RT Reference title
RL Reference data