1. Department of Bioinformatics, University Medical Center Göttingen, Georg August University, D-37077 Göttingen, Germany
2. geneXplain GmbH, D-38302 Wolfenbüttel, Germany
) provides a comprehensive classification of human transcription factors (TFs), based on their DNA-binding domains. Transcription factors constitute a large functional family of proteins directly regulating the activity of genes. Most of them are sequence-specific DNA-binding proteins, thus reading out the information encoded in cis-regulatory DNA elements of promoters, enhancers and other regulatory regions of a genome. TFClass updates earlier attempts to classify eukaryotic transcription factors (1, 2); it is a database that classifies (so far) human transcription factors by a six-level classification schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene products. With this classification, we hope to provide a basis for deciphering protein-DNA recognition codes; moreover, it can be used for constructing expanded transcriptional networks by inferring additional TF-target gene relations.
This work has been partially funded under the EU FP7 programme (contract numbers 202272, LipidomicNet, and 258236, SysCol). In addition, we acknowledge the financial support by a grant from the German Ministry of Education and Research (BMBF grant no. FKZ0315890B, GerontoShield). The authors wish to thank Olga Kel-Margoulis (geneXplain GmbH) for her constant advice, and Volker Matys and Mathias Krull (BIOBASE GmbH) for their help in providing the links to the TRANSFAC database.
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