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footprintDB是目前为止我看到的最全的转录因子数据库

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发表于 2017-3-20 22:52:52 | 显示全部楼层 |阅读模式
看介绍:http://floresta.eead.csic.es/footprintdb/index.php

[size=13.3333px]Current version of footprintDB includes:
  • 7196 Transcription Factors (TFs, 5507 unique)
  • 9087 Position Specific Scoring Matrices (PSSMs, PWMs or DBMs, 8577 unique)
  • 23174 DNA Binding Sites (DBSs, 19850 unique)
[size=13.3333px]extracted from the [size=13.3333px]literature and other repositories[size=13.3333px].

太齐全了:
[size=13.3333px]
Like in this example. The resulting URL will be automatically redirected to the footprintDB entry.


DatabaseVersionTFsMotifsSitesDescriptionAuthorsData
CISBP 11.02187818920Subset of directly determined DNA motifs within the CIS-BP Database.Weirauch MT, Yang A, Albu M et al.
Transcription factors
DNA Binding Motifs

JASPAR 220161307204911414Curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotesMathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, Shi W, Shyr C, Tan G, Worsley-Hunt R, Zhang AW, Parcy F, Lenhard B, Sandelin A, Wasserman WW.
Transcription factors
DNA Binding Motifs

DNA Binding Sites

3D-footprint 320161221142311771545Database of DNA-binding protein structures that is updated weekly with Protein Data Bank complexesContreras-Moreira,B.
Transcription factors
DNA Binding Motifs
DNA Binding Sites
AthalianaCistrome4v4_May20165328380Raw and unmethylated genomic DNA DAP-seq motifs for Arabidopsis thaliana in-vitro-expressed TFs.OMalley RC, Huang SC, Song L et al.
Transcription factors
DNA Binding Motifs

HumanTF 51.05328180Sequence-specific binding preferences of human TFs obtained by high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificitiesJolma A., Yan J., Whitington T., Toivonen J., Nitta K.R., Rastas P., Morgunova E., Enge M., Taipale M., Wei G., Palin K., Vaquerizas J.M., Vincentelli R., Luscombe N.M., Hughes T.R., Lemaire P., Ukkonen E., Kivioja T., Taipale J.
Transcription factors
DNA Binding Motifs

HOCOMOCO 6v94254263073Homo sapiens comprehensive model collection containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low and high-throughput methods.Ivan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic and Vsevolod J. Makeev
Transcription factors
DNA Binding Motifs

DNA Binding Sites

UniPROBE 7201209194114152963Repository of experimental data from universal protein binding microarray (PBM) experimentsNewburger DE, Bulyk ML
Transcription factors
DNA Binding Motifs

DNA Binding Sites

HumanTF2 81.01396630Sequence-specific binding preferences of human TF pairs that bind cooperatively to DNA obtained by CAP-SELEX analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have nJolma A., Yin Y., Nitta K. R., Dave K., Popov A., Taipale M., Enge M., Kivioja T., Morgunova E., Taipale J.
Transcription factors
DNA Binding Motifs

AthaMYB 91.011622416Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast.Kelemen Z., Sebastian A., Xu W., Grain D., Salsac F., Avon A., Berger N., Tran J., Dubrecq B., Lurin C., Lepiniec L., Contreras-Moreira B., Dubos C.
Transcription factors
DNA Binding Motifs
DNA Binding Sites
FlyZincFinger 101.0691410Global analysis of Drosophila Cys2-His2 zinc finger proteinsEnuameh MS et al (Wolfe Lab)
Transcription factors
DNA Binding Motifs

ArabidopsisPBM 1120140210641080Collection of 63 plant TFs representing 25 families, using protein-binding microarrays. Almost half of these TFs recognize secondary motifs, which in some cases were completely unrelated to the primary element. Analyses of coregulated genes and transcriptFranco-Zorrilla JM Lopez-Vidriero I Carrasco JL Godoy M Vera P Solano R
Transcription factors
DNA Binding Motifs

Athamap 12200910287491144AthaMap provides a genome-wide map of potential transcription factor binding sites (TFBS) in Arabidopsis thalianaBulow L, Engelmann, S., Schindler, M., Hehl R.
Transcription factors
DNA Binding Motifs

DNA Binding Sites

DBTBS 131.071901261A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation informationSierro N., Makita Y., de Hoon M.J.L. and Nakai K.
Transcription factors
DNA Binding Motifs

DNA Binding Sites

RegulonDB 147.582821862Curated data of the transcriptional regulatory network of Escherichia coli K12Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J.
Transcription factors
DNA Binding Motifs

DNA Binding Sites

DrosophilaTF 151.16062886Motif models reported in 51 primary references in the form of position PWMs for 56 Drosophila melanogaster transcription factorsDown TA, Bergman CM, Su J, Hubbard TJ
Transcription factors
DNA Binding Motifs

DNA Binding Sites

EEADannot 161.01131110Contreras-Moreira B, Sebastian A.
Transcription factors
DNA Binding Motifs

DNA Binding Sites



1Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014 Sep 11;158(6):1431-43. doi: 10.1016/j.cell.2014.08.009. [Pubmed]
2Mathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, Shi W, Shyr C, Tan G, Worsley-Hunt R, Zhang AW, Parcy F, Lenhard B, Sandelin A, Wasserman WW. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res : (2015). [Pubmed]
3Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic acids research 3891-7 (2010). [Pubmed]
4O'Malley RC, Huang SS, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell 165:1280-92 (2016). [Pubmed]
5Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J. DNA-Binding Specificities of Human Transcription Factors. Cell. 2013 Jan 17;152(1-2):327-39. [Pubmed]
6Kulakovskiy I.V, Medvedeva Y.A, Schaefer U, Kasianov A.S, Vorontsov I.E, Bajic V.B, Makeev V.J. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic acids research 41195-202 (2013). [Pubmed]
7Robasky K, Bulyk ML. UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res. 2011 Jan;39(Database issue)124-8 [Pubmed]
8Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 527:384-8 (2015). [Pubmed]
9Kelemen Z., Sebastian A., Xu W., Grain D., Salsac F., Avon A., Berger N., Tran J., Dubrecq B., Lurin C., Lepiniec L., Contreras-Moreira B., Dubos C. Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast. PLoS One 10, e0141044 (2015). [Pubmed]
10Enuameh MS et al (2013) Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res. 23(6):928-40. doi: 10.1101/gr.151472.112 [Pubmed]
11Franco-Zorrilla J.M, López-Vidriero I, Carrasco J.L, Godoy M, Vera P, Solano R. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proceedings of the National Academy of Sciences of the United States of America : (2014). [Pubmed]
12Bülow L, Engelmann S, Schindler M, Hehl R. AthaMap, integrating transcriptional and post-transcriptional data. Nucleic acids research 37983-6 (2009). [Pubmed]
13Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic acids research 3693-6 (2008). [Pubmed]
14Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado L, Garcia-Sotelo JS, Weiss V, Solano-Lira H, Martinez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernandez S, Alquicira-Hernandez K, Lopez-Fuentes A, Porron-Sotelo L, Huerta AM, Bonavides-Martinez C, Balderas-Martinez YI, Pannier L, Olvera M, Labastida A, Jimenez-Jacinto V, Vega-Alvarado L, Del Moral-Chavez V, Hernandez-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan 1;41(D1)203-D213. [Pubmed]
15Down T.A, Bergman C.M, Su J, Hubbard T.J. Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS computational biology 3:e7 (2007). [Pubmed]
16


[size=13.3333px]DisclaimerThese data are available AS IS and at your own risk. The EEAD/CSIC do not give any representation or warranty nor assume any liability or responsibility for the data nor the results posted (whether as to their accuracy, completeness, quality or otherwise). Access to these data is available free of charge for ordinary use in the course of research.





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