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Transcription factor binding sites represented by Genomatix weight matrices

Introduction

The Genomatix matrix library currently contains more than 1100 weight matrices each representing the DNA-binding sites of a transcription factor (TF) or a transcription factor family. This task enables you to easily check if the transcription factors you are interested in are represented by Genomatix weight matrices, and vice versa.

Currently, transcription factors from several vertebrate species (including human, mouse, and rat) are assigned to the vertebrate group of matrices. Transcription factors from several plant species are assigned to the plant group. Drosophila transcription factors are assigned to the insects group and transcription factors from Saccharomyces cerevisiae and Schizosacchaomyces pombe are assigned to the fungi group of the matrix library.

Parameters

Transcription Factor (TF) -> Weight Matrix Family:

• Enter a TF name or synonym (e.g. Sp1) or a GeneID (e.g. 6667) into the form field and press the button "Get Matrix Family".
• If you are unsure about spelling of the TF try to enter only the first two letters (required) of a TF name or synonym. Wildcards (*) are allowed at the end of the term (e.g. Sp*). In this case, you will receive a list of all TF names and synonyms matching your query that are assigned to a Genomatix weight matrix family. To view the information on a TF, select one synonym from the list and press the button "Get Matrix Family". Wildcards are allowed also for GeneIDs (e.g. 666*).
  
  
• Note: The input is case insensitive (e.g. SP1 is the same as Sp1).

Weight Matrix Family -> Transcription Factor:

• Enter the complete matrix or matrix family name into the form and press the button "Get Transcription Factor". For example, a valid matrix family name is V$SP1F.
• For the complete list of matrices and matrix families, please have a look at the Genomatix matrix library.

Output

If the TF name or GeneID you entered is represented by a Genomatix weight matrix family you will receive a result table containing the name of the weight matrix family, the GeneID, and the organism information of the TF.

If you enter a weight matrix (family) name you will receive a result table containing the names of the transcription factor(s) that are represented by the matrix family, the GeneID and the organism information of the TF(s).