Briefly, AutoMATRIX is a tool to predict key transcription factors in microarray experiments.

The main design goal behind the development of AutoMATRIX was to allow for a convenient and user-friendly identification of transcription factors for observed expression patters. Biologists with microarray and transcription factor expertise should be supported with an appropriate graphical user interface which provides control over an automated workflow for the analysis of experimental results.

The initial input to AutoMATRIX is a list of genes to be analyzed. The genes in such a list are transparently inserted into a mySQL database for further processing. In the next step the user provided upstream regions of the entries in the gene list are loaded into the same database. Afterwards, the MATCH tool is invoked for the PWM analysis of each of the stored upstream sequences. The results of the PWM analyses are stored in the underlying mySQL database for further processing. In order to provide the user with additional information about the identified transcription factors, the relevant data is automatically extracted from TRANSFAC and imported into AutoMATRIX. After these steps the analysis results are displayed in the user interface. A table-based presentation is used for these purposes, where each line contains detailed information about one of the identified transcription factors, such as regulated genes, cell specificity, functional properties and structural features. The factors in a table are sorted by a relevance score which distinguishes between basal and the usually more important gene specific ones.

Furthermore, AutoMATRIX results can be exported into spreadsheets for post-processing with external tools.

Summary

The program undertakes the following steps

• import differentially expressed gene data from the microarray experiment results
• when necessary, map microarray spot identifiers to gene symbols using SOURCE
• retrieve upstream sequences for all genes using gene symbols
• scan upstream sequences for transcription factor binding sites using Match™
• extract relevant information from TRANSFAC^® via a purpose built parser
• show result tables that can be exported to spreadsheet applications

This site is sponsored by Rothamsted Research and The Biotechnology and Biological Sciences Research Council (BBSRC, UK) and is being developed and maintained by scientists at Rothamsted Research