AnimalTFDB 2.0: A resource for expression, prediction and functional study of animal transcription factors

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D76-D81

  Zhang, Hong Mei ^a   Liu, Teng ^a   Liu, Chun Jie ^a   Song, Shuangyang ^a   Zhang, Xiantong ^a   Liu, Wei ^a   Jia, Haibo ^a   Xue, Yu ^a   Guo, An Yuan ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ANIMALTFDB 2.0; ARTICLE; CHROMATIN REMODELING FACTOR GENE; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA ANALYSIS SOFTWARE; GENE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC DATABASE; GENOMICS; HUMAN; NONHUMAN; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN EXPRESSION; SEQUENCE ALIGNMENT; TRANSCRIPTION CO FACTOR GENE; TRANSCRIPTION FACTOR GENE; TRANSCRIPTION REGULATION; ANIMAL; CHEMISTRY; CLASSIFICATION; GENE EXPRESSION; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN DATABASE;

ANIMALS; DATABASES, PROTEIN; GENE EXPRESSION; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ALIGNMENT; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 84941121620     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku887     Document Type: Article

References (40)

1. Jin, J., Zhang, H., Kong, L., Gao, G. and Luo, J. (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res., 42, D1182-D1187.
2. Zhang, H. M., Chen, H., Liu, W., Liu, H., Gong, J., Wang, H. and Guo, A. Y. (2012) AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res., 40, D144-D149.
3. Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A. and Luscombe, N. M. (2009) A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet., 10, 252-263.
4. Guo, A. Y., Chen, X., Gao, G., Zhang, H., Zhu, Q. H., Liu, X. C., Zhong, Y. F., Gu, X., He, K. and Luo, J. (2008) PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res., 36, D966-D969.
5. Charoensawan, V., Wilson, D. and Teichmann, S. A. (2010) Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res., 38, 7364-7377.
6. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L. and Luo, J. (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics, 21, 2568-2569.
7. Kanamori, M., Konno, H., Osato, N., Kawai, J., Hayashizaki, Y. and Suzuki, H. (2004) A genome-wide and nonredundant mouse transcription factor database. Biochem. Biophys. Res. Commun., 322, 787-793.
8. Pfreundt, U., James, D. P., Tweedie, S., Wilson, D., Teichmann, S. A. and Adryan, B. (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res., 38, D443-D447.
9. Fulton, D. L., Sundararajan, S., Badis, G., Hughes, T. R., Wasserman, W. W., Roach, J. C. and Sladek, R. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol., 10, R29.
10. Lee, A. P., Yang, Y., Brenner, S. and Venkatesh, B. (2007) TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. BMC Genom., 8, 441.
11. Zheng, G., Tu, K., Yang, Q., Xiong, Y., Wei, C., Xie, L., Zhu, Y. and Li, Y. (2008) ITFP: an integrated platform of mammalian transcription factors. Bioinformatics, 24, 2416-2417.
12. Wilson, D., Charoensawan, V., Kummerfeld, S. K. and Teichmann, S. A. (2008) DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res., 36, D88-D92.
13. Farrell, C. M., O'Leary, N. A., Harte, R. A., Loveland, J. E., Wilming, L. G., Wallin, C., Diekhans, M., Barrell, D., Searle, S. M., Aken, B. et al. (2014) Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res., 42, D865-D872.
14. Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E. et al. (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov., 2, 401-404.
15. Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csardi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M. et al. (2011) The evolution of gene expression levels in mammalian organs. Nature, 478, 343-348.
16. Merkin, J., Russell, C., Chen, P. and Burge, C. B. (2012) Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science, 338, 1593-1599.
17. Flicek, P., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S. et al. (2014) Ensembl 2014. Nucleic Acids Res., 42, D749-D755.
18. Chatr-Aryamontri, A., Breitkreutz, B. J., Heinicke, S., Boucher, L., Winter, A., Stark, C., Nixon, J., Ramage, L., Kolas, N., O'Donnell, L. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
19. Keshava Prasad, T. S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
20. Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S. et al. (2014) A draft map of the human proteome. Nature, 509, 575-581.
21. Wilhelm, M., Schlegl, J., Hahne, H., Moghaddas Gholami, A., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H. et al. (2014) Mass-spectrometry-based draft of the human proteome. Nature, 509, 582-587.
22. Li, J. J., Huang, H., Bickel, P. J. and Brenner, S. E. (2014) Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Res., 24, 1086-1101.
23. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. and Salzberg, S. L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
24. Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L. and Pachter, L. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol., 31, 46-53.
25. Zhang, S. J., Liu, C. J., Yu, P., Zhong, X., Chen, J. Y., Yang, X., Peng, J., Yan, S., Wang, C., Zhu, X. et al. (2014) Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque. Mol. Biol. Evol., 31, 1309-1324.
26. Zhang, S. J., Liu, C. J., Shi, M., Kong, L., Chen, J. Y., Zhou, W. Z., Zhu, X., Yu, P., Wang, J., Yang, X. et al. (2013) RhesusBase: a knowledgebase for the monkey research community. Nucleic Acids Res., 41, D892-D905.
27. McDowall, J. and Hunter, S. (2011) InterPro protein classification. Methods Mol. Biol., 694, 37-47.
28. Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
29. Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N. et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140, 744-752.
30. Finn, R. D., Clements, J. and Eddy, S. R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
31. Schaefer, U., Schmeier, S. and Bajic, V. B. (2011) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res., 39, D106-D110.
32. Huminiecki, L. and Heldin, C. H. (2010) 2R and remodeling of vertebrate signal transduction engine. BMC Biol., 8, 146.
33. Conant, G. C. and Wolfe, K. H. (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet., 9, 938-950.
34. Gillis, W. Q., St John, J., Bowerman, B. and Schneider, S. Q. (2009) Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family. BMC Evol. Biol., 9, 207.
35. Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S. and Van de Peer, Y. (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol., 7, R43.
36. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
37. Lim, A. and Zhang, L. (1999) WebPHYLIP: a web interface to PHYLIP. Bioinformatics, 15, 1068-1069.
38. Crooks, G. E., Hon, G., Chandonia, J. M. and Brenner, S. E. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
39. Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J. F., Guindon, S., Lefort, V., Lescot, M. et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res., 36, W465-W469.
40. Xie, C., Zhang, Y. E., Chen, J. Y., Liu, C. J., Zhou, W. Z., Li, Y., Zhang, M., Zhang, R., Wei, L. and Li, C. Y. (2012) Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet., 8, e1002942.