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

List of available transcription factors

This list contains all loaded transcription factor profiles, including those from JASPAR and any loaded by the user. Profiles are transferred to the "Selected TF" list just below by double-clicking on them in the list.

• Search - search the list items for the input characters

• Find Next - continue scanning the list for the next occurrence of the search characters.

Selected TF

This list contains the profiles that will be used in the next search. Items are moved onto this list by double clicking their entries in the TF Mapping list above. Entries on the Selected TF list can be moved back up to the "TF Mapping" list by again double clicking on their entry.

Here the TATA-box entry has been moved to the selected list by double-clicking its entry in the list of available TFs.

Controls

• Scan - start the scan of the current nucleotide sequence with the selected profiles.

• Add TF - load a new profile from a file into the list of available profiles. This is not a permanent addition; it remains loaded only for the current invocation of geWorkbench. The profile should consist of a tab delimited series of counts, one for each position in the profile. It should could four lines, in the order A, C, G, T. There are no header lines or row labels, just the numeric matrix. For example, here is a profile showing the first six columns:

0 12 0 0 1 0

49 0 20 23 3 45

0 37 29 2 45 4

0 0 0 25 0 0

• Save - Saves a list of hits by a profile to a nucleotide sequence, including the sequence identifier and the start and stop points of the match along the sequence, as shown here:

gi|65508003

ATHB5:HOMEO-ZIP:MA0110 2104 2113

ATHB5:HOMEO-ZIP:MA0110 2115 2106

ATHB5:HOMEO-ZIP:MA0110 2882 2891

ATHB5:HOMEO-ZIP:MA0110 2893 2884

• Retrieve - Not implemented.
• Stop - Stop the current scan.

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.