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Transcription factor


Transcription factor overview

The transcription factor overview can be accessed by selecting the 'transcription factors (all)' section for browsing. As there are several thousand transcription factor entries in MatBase, this might take a while to display, depending on your browser and your network connection. You can also choose to only display human, mouse, rat, plant or yeast transcription factors (you can use the search field to get all transcription factors for other organisms or specific plants). Entries are ordered by the official EntrezGene symbol of the gene listed in the first column. Moreover a short description of the gene is listed as well as the organism(s) for the gene and any associated matrix families. For transcription factors that do not bind a specific DNA pattern or do not bind DNA at all the last column contains one or more transcription factor categories describing the nature of the factor. (See below for a list.)

To find a specific entry, we recommend using the search feature of MatBase rather than browsing the complete list. You can, however, try to locate your gene of interest by using the 'find' or 'search' functionality of your browser (usually accessed by pressing ctrl-f on Windows or Unix or option-f on a Mac).

Clicking on a transcription factor name will take you directly to the 'transcription factor result'. Clicking on a matrix family name will take you to the 'matrix family result'.

transcription factor overview

Homology groups

If you search for a transcription factor by name or gene id, the result page will show just a single entry for all genes with the same symbol. Clicking on the name will take you to the 'Homology groups' page. This page lists genes from all organisms that match the name pattern. It also shows any additional genes that are homolog to any of these. The screenshot below shows a simple example where all genes named 'Ahr' belong to the same homology group. Sometimes you will encounter results where the genes listed do not all belong to the same homology group, or some do not belong to a homology group at all. This means, that overall sequence similarity between the genes is not high enough to assert the homology of the gene. This is sometimes due to inaccurate gene annotation but may also be due to a real sequence dissimilarity between different species. Homology information is taken from the ElDorado database and is generated by a proprietary algorithm.

The entries in the table are ordered by organism. The official symbols are listed in the second column, followed by a short description of the gene. The 'Synonyms' column lists all known synonyms of the gene name, separated by a semicolon. Any associated matrix families can be found under 'Associated families'. For transcription factors that do not bind a specific DNA pattern or do not bind DNA at all this column contains one or more transcription factor categories describing the nature of the factor. (See below for a list.)

Clicking on a transcription factor symbol will take you directly to the 'transcription factor result'. Clicking on a matrix family name will take you to the 'matrix family result'. Clicking the 'ElDorado' link in the 'More info' column will take you to the 'More gene info' page of ElDorado. Clicking the 'EntrezGene' link will take you to the NCBI's EntrezGene database entry for the gene. Clicking a 'Mendel' link (not shown in the screenshot) will take you the the Mendel database entry of the gene.

homology groups

Transcription factor result page

In contrast to the homology groups page above, the 'Transcription factor result page' shows you the information for a single gene from a single organism. (The screenshot below has been altered to only show nine different gene <-> gene interactions.)

transcription factor result

Information on the result page:

Symbol: This is the official gene symbol from NCBI's EntrezGene database. Please note that several plant genomes are not yet included in EntrezGene. For these the symbol has been taken either from the Mendel database or from literature.
Organism: The latin and the common name (in parentheses) of the species this gene belongs to.
GeneID: NCBI's Gene ID, if available.
Description: A short description of the gene.
Synonyms: All known synonyms for this gene, separated by semicolon. These are also used when searching MatBase, so you can enter a synonym instead of the official symbol to find a gene.
Associated matrix families: Lists any matrix families associated with this transcription factor (i.e. there is one or more weight matrix descriptions allowing you to search for potential binding sites of this factor using MatInspector). Clicking on the family name will take you the the 'family result'. For transcription factors that do not bind a specific DNA pattern or do not bind DNA at all one or more categories from the following list are given:
  • general transcription factor (PolI)
  • general transcription factor (PolII)
  • general transcription factor (PolIII)
  • transcription initiation factor (TIF)
  • transcription elongation factor
  • transcription termination factor
  • TBP associated factor
  • TBP associated factor (PolI specific)
  • TBP associated factor (PolII specific)
  • TBP associated factor (PolIII specific)
  • transcription cofactor
  • mediator
  • ATP-dependent chromatin remodelling
  • histone modification
  • acetyltransferase
  • deacetylase
  • methyltransferase
  • demethylase
  • protein kinase
  • protein phosphatase
  • poly(ADP)ribosylase
  • ubiquitin ligase
  • SUMO ligase
  • poly(ADP-ribosyl)transferase
  • polycomp group
  • trithorax group
Homolog transcription factors: Lists all homologous transcription factors for this gene including the species. Clicking on a transcription factor symbol will take you to result page for the homolog transcription factor.
Gene <-> Gene Interactions: Lists all gene <-> gene interactions where the transcription factor shown either acts as a regulator for another gene or is regulated by another gene. Both genes are listed, as well as the type of interaction. For more information on the genes involved click on the gene symbol to go the "More Gene Info" page of ElDorado. If both genes are transcription factors, this is indicated by 'TF <-> TF' in the fourth column of the table. For more detailed information on the evidence for interaction click the 'more...' link in the last column.

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