TRANSFAC® release 2017.2
The TRANSFAC® database on transcription factors, their genomic binding sites and DNA-binding motifs (PWMs), contains these new data features:
- 528 new matrices (DNA-binding motifs) for Arabidopsis thaliana transcription factors based on DAP-Seq (DNA affinity purification sequencing) (O’Malley et al., 2016 Cell 165: 1280-1292) and 46 matrices for Arabidopsis thaliana transcription factors based on PBM (protein binding microarrays) (Sullivan et al., 2014 Cell Rep. 8:2015-2030).
- 521 DAP-Seq data sets from the Arabidopsis cistrome database comprising 2,826,587 fragments (O’Malley et al., 2016 Cell 165: 1280-1292) analyzed with the MATCH tool for 2,682,764 best binding sites inside the fragments.
- 253 new transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 3 project between October 2016 and January 2017. The data sets comprise 4,622,342 fragments bound by 213 distinct transcription factors, of which 157 factors were not yet covered by ChIP-Seq data. For 142 of the sets, an existing positional weight matrix for the respective transcription factor was used together with the MATCH tool to predict altogether 2,841,686 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.
- Genomic information for genes, promoters, and ChIP fragments for the species human, mouse, rat, macaque, and Arabidopsis is now based on Ensembl release 87.
- New November 2016 dbSNP data releases for human and rat have been integrated.
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 2017.2 (download; pdf, 68 KB)
TRANSFAC® Statistics 2017.1 (download; pdf, 68 KB)
TRANSFAC® Release 2017.2 (download; pdf, 162 KB)
TRANSFAC® Release 2017.1 (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