geWorkbench

Overview

The Promoter component scans one or more sequence profiles against nucleotide sequences that the user has loaded into geWorbench. Motifs from the JASPAR database of transcription factor binding sites are included with the component. Additional motifs can be added by the user.

The Promoter component will also display the results of hits found in the Pattern Discovery component.

JASPAR CORE database

The motif datafile currently included with geWorkbench is version 3.0 of the JASPAR CORE database (http://jaspar.genereg.net/) . It contains 138 curated, non-redundant profiles. These "profiles are derived from published collections of experimentally defined transcription factor binding sites for multi-cellular eukaryotes. The database represents a curated collection of target sequences" (JASPAR Documentation).

The datafile used "MATRIX_DATA.txt" found at http://jaspar.genereg.net/html/DOWNLOAD/mySQL/JASPAR_CORE_2008/. This file is stored within the Promoter component of geWorkbench.

The profiles are represented by counts of how many times each of the four nucleotide bases occurs at a particular position in the aligned sequences.

Working with the Promoter graphical interface

Layout

The figure shows the display of profile "TBP:TATA-box:MA0108" from the list of those included in JASPAR.

TF Mapping

Search

Find Next

Selected TF

Scan

Add TF

Save

Retrieve

Stop

The LOGO tab

LOGO display

The LOGO display implements the method of Schneider to display the information at each position in a motif. Briefly, the total height of the column of letters at a position shows the information available, on a scale of 0 to 2 bits (the information needed to represent the 4 possible nucleotide bases at each position). The relative heights of each letter in a column show their individual contribution to the information at that position.

The LOGO display in geWorkbench implements the "small sample correction" described by Schneider, the magnitude of which depends on the number of sequences aligned to generate the profile. The correction is subtracted from the calculated information content at each position, with a minimum value (floor) of zero being displayed.

Table display

A table is used to show the numeric data from which the LOGO diagram is generated. The table depicts each position in the profile as a column, and has a row for each of the four nucleotide bases A, C, G and T. The user can choose to display the data either as the original counts or as frequencies.

• Display: Counts or Frequencies

The Parameters tab

The Sequence tab:

Running and viewing a scan

1. Hit Scan.
2. Check the box "Show TFs".
3. Hits of this motif against the sequences are displayed in the sequence window.

References

Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. Jan 1;32(Database issue):D91-4 (link to paper).

Schneider TD, Stephens RM. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. Oct 25;18(20):6097-100. (link to paper)

Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. Jan 1;34(Database issue):D95-7.