TRANSFAC® release 2017.3
The TRANSFAC® database on transcription factors, their genomic binding sites and DNA-binding motifs (PWMs), contains these new data features:
- Annotation of transcription factor binding sites based on sequence conservation
Known transcription factor binding sites located in human, mouse or rat genomes were extracted from TRANSFAC® and highly conserved sites were retained. Given high conservation as a prerequisite, binding sites were annotated for the two 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 1,565 new binding site entries.
- ChIP-Seq experiment browse pages
New browse page for 161 human DNase hypersensitivity ChIP-Seq experiments imported from ENCODE. The genomic intervals for each data set can be downloaded in .BED format.
The TFBS and DNase ChIP-Seq experiment browse pages can be accessed from the tools menu. The BED download buttons have also been added to the TFBS ChIP-Seq experiment browse page, providing easier access for the now 2,032 data sets.
113 new transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 3 project between February 2017 and May 2017 https://www.encodeproject.org/matrix/?type=Experiment&status=released. The data sets comprise 1,329,758 fragments bound by 98 distinct transcription factors, of which 66 factors were not yet covered by ChIP-Seq data. For 71 of the sets, an existing positional weight matrix for the respective transcription factor was used together with the MATCH tool to predict altogether 816,574 best binding sites inside the fragments. Predicted best binding sites as well as complete fragments are available in FASTA and BED format via the ChIP Experiment Reports, as are lists of genes in a distance range to the fragments as specified by the user.
- Reorganization of the in vivo transcription factor bound fragment section on a Locus Report
To improve clarity, only those fragment are listed that overlap with one of the promoter sequences of the entry. As new information fields, the table contains the relative position of the fragment to the transcription start site (TSS) of promoter, as well as the sequence of the predicted best binding site for the transcription factor inside the fragment.
- HOCOMOCO v10 matrix library integration
134 mononucleotide position weight matrices based on ChIP-Seq experiments have been incorporated from HOCOMOCO v10 (http://hocomoco.autosome.ru/).
- Enhanced human SNP content
The new March 2017 dbSNP Build 150 data for human has been integrated and increases the number of SNPs mapped to human promoter sequences more than two-fold from 34,839,288 in the last release to 73,423,232.
Genomic information for genes, promoters, and ChIP fragments for the species human, mouse, rat, macaque, and Arabidopsis is now based on Ensembl release 89.
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., 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
TRANSFAC® Flyer (download; pdf, 63 KB)
TRANSFAC® Statistics 2017.3 (download; pdf, 68 KB)
TRANSFAC® Statistics 2017.2 (download; pdf, 68 KB)
TRANSFAC® Release 2017.3 (download; pdf, 579 KB)
TRANSFAC® Release 2017.2 (download; pdf, 162 KB)
TRANSFAC® Documentation (download; pdf, 71 KB)
TRANSFAC® Video (at YouTube)
See also the TRANSFAC® entry at Wikipedia.
More about TRANSFAC as a scientific project and its history on the pages of Edgar Wingender.
TRANSFAC® is a registered trademark of QIAGEN.
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