Introduction

The prediction of specific transcription factor target genes is a major challenge in systems biology and functional genomics. Current sequence-based methods yield many false predictions, due to the short and degenerated DNA-binding motifs. We provide a tool for a new systematic genome-wide approach using the seed-distribution-distance method, that searches large-scale genome-wide expression data for genes that are similarly expressed as known targets. This method allows to identify genes that are likely targets, allowing sequence-based methods to focus on a subset of genes, giving rise to fewer false-positive predictions. ...

What do you need to provide

• list of known target genes

What do you get

• ranked list of genes with names and links to Ensembl and NCBI
• detailed information about the mapping of your data to the internal database
• cross-validation with a recovery test (graphical output and raw data)
• List of potential new targets filtered according to binding affinity of given transcription factors   

How does it work?

The overall idea of targetfinder.org is that genes that share a transcription factor binding site in their promoter are co-regulated. If a user of targetfinder.org provides a list of genes which he knows are regulated by a certain transcription factor, targetfinder.org searches for genes that show a similarly expression pattern in a large microarray pannel of more than 1200 experiments. A second property, the binding affinity is used to give a combined prediction of potential new targets.