TRANSFAC® release 2019.2
The TRANSFAC® database on transcription factors, their genomic binding sites and DNA-binding motifs
(PWMs), contains these new data features:
- Matrices for methylated binding motifs
1,785 matrices for human transcription factors from Methyl-HT-SELEX and HT-SELEX experiments
were added. They were published in “Yin, Y. et al, Impact of cytosine methylation on DNA binding
specificities of human transcription factors, Science 2017 356(6337):eaaj2239, Pubmed PMID:
Based on the selection of representative methylated motifs, a specific matrix profile has been
added to be used with MATCH.
- Drosophila melanogaster promoters added
19,152 promoters for fruit fly (Drosophila melanogaster) have been included based on data from
Ensembl version 95 and our established virtual transcription start site calculation. Experimentally
verified transcription factor binding sites and 3.6 million SNPs from the dbSNP database have
been mapped to the promoter sequences.
- Annotation of transcription factor binding sites based on sequence conservation
Known transcription factor binding sites located in human, mouse, rat, or pig genomes
were extracted from TRANSFAC® and highly conserved sites were retained. Given high
conservation as a prerequisite, binding sites were annotated for the three other species in
respective genomic location if not more than one mismatch was observed in the
sequence alignment with the primary species. This resulted in 1,007 new binding site
- Integration of new human and fruit fly ChIP-Seq experiments from ENCODE, modENCODE and
21 new human transcription factor binding site ChIP-Seq experiments released by the ENCODE
phase 3 and 4 project between July 2018 and December 2018 have been integrated. The data sets
comprise 424,961 fragments bound by 15 distinct transcription factors.
For Drosophila melanogaster, 470 transcription factor binding site ChIP-Seq experiments released
by the modENCODE and modERN were added. The data sets include 2,050,835 fragments bound
by 411 distinct transcription factors, all of which were not yet covered by TRANSFAC ChIP-Seq
For 183 of the sets, an existing positional weight matrix for the respective transcription factor was
used together with the MATCH tool to predict altogether 953,185 best binding sites inside the
- Ensembl version update
Genomic information for genes, promoters, and ChIP fragments for the species human, mouse,
rat, pig, macaque, Drosophila, and Arabidopsis is now based on Ensembl release 95.
Thank you very much for your interest in our programs!
Please contact us and you will be provided with your free trial version.
Learn more about promoter analysis with TRANSFAC® in the geneXplain platform.
Most transcription factors (TFs) possess a DNA-binding domain (DBD), which mediates the recognition of specific, short DNA sequence elements in promoter, enhancer, etc. In order to approach the problem of deciphering the underlying DNA-protein recognition code, we have completely revised an earlier TF classification scheme (1,2) by adapting it to the wealth of data that were reported during the last ten years (TFClass; 3-5). TFClass has been implemented at the Dept. of Bioinformatics at the University Medical Center Göttingen (3,6).
Part of this work was done in the context of the Syscol
project, where our partner at the Karolinska institute (Prof. J. Taipale and his team) have characterized the DNA-binding profiles of more than 400 mammalian TFs (7). It will be tempting to compare the similarities of their matrices with the DBD classification reported here, and with our own approaches to classify DNA-binding profiles (8).
- Wingender, E., Schoeps, T., Haubrock, M., Krull, M. and Dönitz, J. (2018) TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 46, D343-D347. Link
- Wingender, E., Schoeps, T., Haubrock, M., Dönitz, J. (2015) TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res. 43, D97-D102. Link
- Stegmaier, P., Kel, A., Wingender, E., Borlak, J. (2013) A discriminative approach for unsupervised clustering of DNA sequence motifs. PLoS Comput. Biol. 9, e1002958.
- Jolma, A., et al. (2013) DNA-Binding Specificities of Human Transcription Factors. Cell, 152, 327–339. Link
- Wingender, E. (2013) Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol. 11, in press. Link
- Wingender, E., Schoeps, T., Dönitz, J. (2013) TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170. Link
- Heinemeyer, T., Chen, X., Karas, H., Kel, A.E., Kel, O.V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F., Wingender,E. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res., 27, 318–322. Link
- Wingender, E. (1997) Classification scheme of eukaryotic transcription factors. Mol. Biol. Engl. Tr. 31, 498-512. Link
Wingender, E., Schoeps, T., Haubrock, M., Krull, M. and Dönitz, J. (2018) TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 46, D343-D347. PubMed.
Kaplun, A., Krull, M., Lakshman, K., Matys, V., Lewicki, B., Hogan, J.D. (2016) Establishing and validating regulatory regions for variant annotation and expression analysis. BMC Genomics 17 (Suppl. 2):393. PubMed.
Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform. 9:326-332. PubMed.
Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A.E., Wingender, E. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34:D108-D110. PubMed.
Kel, A.E., Gössling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V., Wingender, E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31:3576-3579. PubMed
Wingender, E., Dietze, P., Karas, H., Knüppel, R. (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 24:238-241. PubMed
Knüppel, R., Dietze, P., Lehnberg, W., Frech, K., Wingender, E. (1994) TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J. Comput. Biol. 1:191-198. PubMed
Wingender, E. (1988) Compilation of transcription regulating proteins. Nucleic Acids Res. 16:1879-1902. PubMed