Gene Regulation

TRANSFAC^® Release 7.0 - Documentation

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Latest Changes

Release 7.0 GENE:

RG - regulation of the gene (where and when it is expressed)
CE - list of composite elements with (relative) positions
DR - new links to HumanPSD^TM (BKL), TRANSPRO^TM, UniGene, Ensembl, Affymetrix, EntrezGene (replacing LocusLink), HGNC, MGD, RGD

FACTOR:

FT - automatically assigned domains from Pfam, SMART, and Prosite
DR - new links to HumanPSD^TM (BKL), DATF
(for Arabidopsis)

SITE:

DR - new links to TRANSPRO^TM (TRANSPATH^® links removed, to be found in GENE)

CLASS:

CL - links to the respective nodes in the hierarchical factor classification added

CELL:

BS - new links to sites, which are detected with a binding activity from this "factor source"
DR - new links to TRANSCompel^®

Release 6.0

GENE:

FA - link to encoded factor
BS - regulating factors alongside their binding sites
SY - synonyms for gene name
CH - chromosomal location
DR - (new) links to LOCUSLINK, REFSEQ, OMIM, BRENDA, TRANSPATH^®, PathoDB^®, SMARt DB^TM (and to TRRD and TRANSCompel^TM, which used to be in the separate fields TR and CO)
RN, RX, RA, RT, RL - references with PubMed link

FACTOR:

EX - Expression pattern (for human and mouse starting to replace CP/CN fields of tissue specificity)
GE - link to encoding gene
BS - target gene alongside genomic binding site
DR - new links to RSNP, TRANSPATH^®, PathoDB^® and SMARt DB^TM

SITE:

DR - new links to TRANSPATH^®, PathoDB^® and TRANSCompel^TM

Release 4.0 CELL:

DR line added for external database links and as an additional external data source CLDB entries have been cross-referenced.

Release 3.5

ALL TABLES:

RX line with the MEDLINE ID in the references

FACTOR:

SF - Structural features: Hyperlinks to Factors available.

SITE:

MX - Sites which have been used to construct a matrix exhibit a link to the corresponding MATRIX entry.

MATRIX:

BS - Sites which have been used to construct a matrix are linked

Release 3.4

ALL TABLES:

The two-letter field denominators are linked now to the corresponding explanations given in the documentation.
Enhanced efforts made by the TRANSFAC^® team to improve data quality are described in the "TRANSFAC^® reports". They have been introduced as new reference source which is properly linked wherever appropriate.

SITE:

Some consensus entries in the SITE table can be retrieved by the licensed version only.

FACTOR:

Links to external data sources adding more specific information to individual transcription factors have been introduced in the field "functional features" (FF) (e. g., see T02076).

Release 3.3

FACTOR:

The GENE table not only displays the accession numbers of corresponding SITEs, but gives the positions of the sites as an ordered list and visualizes them using a colour code.
Similarly, positional features of the FACTOR feature table are visualized between the FT and the SF lines.

SITE:

Some consensus entries in the SITE table can be retrieved by the licensed version only.

Release 3.2

FACTOR:

As an additional external data source, PDB entries have been cross-referenced.
At the end of the CL line (CLASS), a systematic decimal classification number has been introduced in numerous FACTOR entries.

Release 3.1 SITE:

As an additional cross-reference to external databases, EPD codes (Eukaryotic Promoter Database) have been included.

FACTOR:

Between SZ (Size) and FT (Feature table), SQ (the amino acid sequence) and SC (Sequene comment) have been inserted.

GENE:

Contains a new table, GENE, which can be used to link TRANSFAC^® with TRRD and, in near future, with EPD.

SITE:

The DE line now also contains the cross-reference to the GENE table.
A new field has been introduced: RE (Gene region), between the Description (DE) and the Sequence (SE) lines.
The CC (comments) lines have been shifted and are now between the Methods (ME) and References (RN) lines.
The DR (external database cross-references) appear now between CC and RN lines.

FACTOR:

Features referring to a known range of positions are given now in a separate field (FT, Feature Table). Structural Features (SF) focuses now on global structural properties.
Cell Specificity (previously CS) has been split into positive (CP) and negative (CN) data on the cellular occurrence of the factors.
An increasing amount of individual statements in CP, CN, FT, SF, FF lines is referring to the literature listed at the end of each entry.
The order of the fields has changed!

MATRIX:

A short description of the factor the matrix refers to has been introduced (SD).