TRANSFAC® Release 7.0 - Documentation

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 HumanPSDTM (BKL), TRANSPROTM, UniGene, Ensembl, Affymetrix, EntrezGene (replacing LocusLink), HGNC, MGD, RGD

FACTOR:

  • FT - automatically assigned domains from Pfam, SMART, and Prosite

  • DR - new links to HumanPSDTM (BKL), DATF
    (for Arabidopsis)

SITE:

  • DR - new links to TRANSPROTM (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 DBTM (and to TRRD and TRANSCompelTM, 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 DBTM

SITE:

  • DR - new links to TRANSPATH®, PathoDB® and TRANSCompelTM

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.

Release 3.0

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).

 

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