GENE
Contents

The GENE table is a central table for all of our databases, now including links to TRANSFAC® and TRANSCompel® tables as well as links to TRANSPATH®, PathoDB® and S/MARt DBTM. It contains all genes for which information is contained in (at least) one of the databases ( Statistics   Statistics). A GENE entry lists all links to individual sites, within DNA or mRNA, (and to their binding factors) given in TRANSFAC® and to the composite elements given in TRANSCompel® along with their positions within the gene. Where appropriate, links to encoded FACTORs (transcription factors or miRNAs) in TRANSFAC® are given as well. In addition to these internal links, links to a growing number of external databases such as ENTREZ, RefSeq, and OMIM are given. Further, the GENE table contains the promoter classification number as proposed by P. Bucher as well as other information.
Fields

It should be noted that in individual entries some fields may be empty. In this case, these fields are not displayed.
AC Accession number   "G" + 6-digit number
AS Accession numbers, secondary   when two or more entries are merged, the additional accession numbers, separated by commas, are stored in this field
ID Identifier   {species acronym}${gene acronym}
DT Created
Updated		   date of entry creation; entry author
date of last entry updating; updater
SD * Short description   short gene term
DE * Description   explicit name of the gene
SY * Synonyms   alternative names of the gene
OS Species   biological species
OC Taxonomic classification   systematic biological classification of the species
CH Chromosomal location   chromosome and locus of the gene
HG Host gene   Gene in which the (miRNA-encoding) gene is located.
IG Intronic gene   Gene (encoding for miRNA) which is located within this gene.
BC EPD Promoter classification   decimal classification number according to P. Bucher's promoter classification system
RG Regulation   where and under what conditions the gene is expressed
BS Binding sites / Binding factors   site positions (normally, relative to the transcription start site, but there may be other reference points, which are then stated in the individual site entries) and linked site accession number; site identifier; Binding factors: factor name linked factor accession number
BR Binding region (ChIP-chip)   DNA fragment from ChIP-on-chip experiments (linked accession number; upstream/downstream from the gene; biological species.)
CE Composite element   positions and accession number of composite element from TRANSCompel.
FA Encoded factor   linked factor accession number; factor name. (for genes encoding a transcription factor or miRNA)
DR External database links   database name (ENTREZGENE, ENSEMBL, UNIGENE, REFSEQ, TRANSPRO, EMBL, OMIM, BKL, TRANSPATH, SMARtDB, PathoDB): database accession number, identifier (where available).

HGNC, MGI, or RGD: standard gene symbol for human, mouse, or rat gene, respectively.

AFFYMETRIX: chip: probeset.
(except for those from chip HuGeneFL, the Affymetrix links are based on those in Ensembl, v.14.31 for human and v.14.30 for mouse)

BRENDA: BRENDA_EC_no.; BRENDA_species_EC_no.
RN Reference number   [consecutive entry reference number]; reference accession number.
RX PUBMED; link to PubMed entry.
RA Reference authors authors (NOTE: accents are omitted, German umlauts are transcribed as follows: ä -> ae, ö -> oe, ü -> ue; German "s-z" (ß) -> ss)
RT Reference title reference title (NOTE: Greek letters are expanded to alpha, beta, gamma etc.)
RL Reference source journal volume:pages (year)

* These fields are commonly searched

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