TRANSPATH Professional Documentation

GENE

Gene

Gene infomation in TRANSPATH^® was formerly provided in the molecule table. To have a clear separation between genes and gene products, they are now stored in a separate table. All genes are linked to the TRANSFAC^® Gene table, where users can find information about the structure of gene regulatory regions, including individual binding sites for transcription factors, and other information as well. Gene entries have hyperlinks to UniGene and Entrez Gene, the human ones also to OMIM and Affymetrix microarray chips. Genes have been included to provide information about the last step in signal transduction pathways: the regulation of target genes by activated transcription factors. Thus, TRANSPATH^® presents information about complete signaling pathways: starting with the activation of a receptor at the membrane through a cascade of kinases into the nucleus, where a particular transcription factor is activated and regulates a set of target genes.

The link between a gene and its gene product(s) is given via reactions with the effect 'expression'. Since the expressed proteins can be signaling molecules or transcription factors themselves, this information is an important step to include feedback loops in signaling networks.

Fields

It should be noted that in individual entries, some fields may be empty. In this case, these fields are not displayed.

Field		Content and format
AC	Accession number	The accession number is the unique identifier for each entry. Its format is "G" followed by six digits (e.g. G012345). If two entries have to be merged, the AC of the primary name is retained. The other AC will be stored in the secondary accession numbers (AS) field.
AS	Accession numbers, secondary	The secondary accession numbers are optional alternate identifiers for each entry. They are of the form defined separated by semicolons, and are created when two entries are merged. The former molecule table accession number is also given here.
DT	Created by	The name of the curator who created the entry. E-mail your feedback directly to the curator.
DT	Updated by	The name of the curator who last updated the entry. E-mail your feedback directly to the curator.
CO	Copyright-information
NA	Name	A short name for the gene, such as the HGNC symbol. It corresponds to the short description for the respective gene in TRANSFAC. A hyperlink with the TRANSFAC accession number is provided in front of the name. There are tags appended to the name to differentiate the species the gene comes from. This short identifier is useful in reaction names because molecules and genes from different species often interact due to the experiments. List of species tags Queries with the search field name automatically include the fields fullname and synonyms.
SY	Synonyms	Alternative names for the gene. This is needed because the names in biosciences change often. The field lists other names or abbreviations. Different synonyms are separated by a semicolon. The field synonyms is automatically included if you run a query with the search field name.
TY	Type	The type of this gene entry. Possible terms are: orthogene, group entry for homologous genes in different species basic, for taxa-specific genes (mostly species-specific, but also higher taxa e.g. mammalia)
NP	NetPro entry	The corresponding NetPro™ entry.
ME	Gene product	Proteins encoded by this gene.
HP	Superfamilies	Lists all groups (orthogene entries) this gene belongs directly to.
HC	Subfamilies	Lists all basic gene entries.
OS	Species	The species that the gene entry belongs to. Given is the common name (if it exists), followed by the Latin denomination, as it is done in TRANSFAC.
DR	External database hyperlink	Database name (e.g. EMBL/GenBank/DDBJ): database accession number; identifier.
XB	Reaction upstream	A list of reactions that lead to this gene. Here the gene serves as a signal acceptor. Up to now, these are all semantic transregulation reactions
XA	Reaction downstream	A list of semantic expression reactions that go out from this molecule.
RN	Reference number	[consecutive entry reference number]. A list of the papers from which the information in this entry was extracted. For further information please see: Reference.
RX	Medline database hyperlink	The PMID number in PubMed
RA	Reference author(s)	list of authors Reference
RT	Reference title	Reference
RL	Reference publication	Reference