TRANSFAC is the database of eukaryotic transcription factors (and miRNAs), their experimentally determined genomic binding sites and derived DNA-binding motifs (PWMs). TRANSFAC allows to search for transcription factor targets based on experimentally determined TF-binding sites, as well as to predict putative transcription factor binding sites (TFBS) in regulatory regions.

The PROTEOME database includes HumanPSD, with focus on gene ontology data, expression patterns and, particularly, association of human (and mouse) genes with diseases and their potential use as biomarkers, as well as
clinical trial information (disease - clinical study - drug links). PROTEOME further includes TRANSPATH, a database on mammalian signal transduction and metabolic pathways. PROTEOME can be applied for functional and network analysis.

Integrated under one web interface, TRANSFAC and PROTEOME, allow seamless analysis with the included gene regulation and functional analysis tools.

This session will be focused on the following topics:

• Brief Introduction to the TRANSFAC+PROTEOME user interface.

• Standard search, custom search, ontology search
• Anatomy of the reports
• Further working with the search results

• Transcription factor binding site (TFBS) search in details.

• Default profiles of matrices
• Customized profiles of matrices
• Options to upload gene lists
• Upload of DNA sequences, which formats can be uploaded
• Example of promoter analysis
• Example of ChIP-seq data analysis

• Introduction to the PathFinder

• Visualization of pathways in different layouts
• Overlay of disease information on pathways
• Overlay of other ontologies on pathways.
• Functional Analysis
• Network Analysis

Presenters: Dr. Volker Matys, Dr. and Olga Kel-Margoulis, PhD