nar db 2010
Posted by razor | Filed under Bioinformatika, English, Szolgáltatás
The Nucleic Acids Research 2010 Database Issue is out with 58 new, and 73 updated databases. The full online collection now contains 1230 databases. Besides the usual stuff, like updates on the NCBI, EBI, GeneBank or GeneOntology databases, it now contains descriptions of various resources in Japan, a new database from Slovakia, and lengthy discussions of databases previously described only briefly.
I picked a few articles, mainly dealing with transcription, transcriptional regulation, transcription factors and binding sites.
The DBTSS database contains information on the transcription start sites of human and mouse genes. These start sites, contrary to the university textbooks, and quite a few articles, are dynamically changing in various cell types and conditions. The latest update contains data of 330 million tags generated by sequencing the 5′ end of cDNAs.
JASPAR is an open-access database of transcription factor binding sites. With the latest update, it contains 457 curated, high-quality, non-redundant binding sites.
The Ensembl Genomes database integrates a huge amount of information from various sources. Besides vertebrates, it now contains data on Metazoa, Protists, Bacteria, Fungi and Plants.
The Plant Transcription Factor Database describes a number of transcription factors from various plant species, from red algae to eudicots. The annotation of the proteins, their classification, 3D structures, alignments, references and cross references to other databases are available at the website.
Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki and Kenta Nakai (2010) DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Research, vol. 38, Database issue, D98-D104; doi:10.1093/nar/gkp1017
Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman and Albin Sandelin (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Research, vol. 38, Database issue, D105-D110; doi:10.1093/nar/gkp950
P. J. Kersey, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kähäri, R. J. Kinsella, E. Kulesha, U. Maheswari, K. Megy, M. Nuhn, G. Proctor, D. Staines, F. Valentin, A. J. Vilella and A. Yates (2010) Ensembl Genomes: Extending Ensembl across the taxonomic space. Nucleic Acids Research, vol. 38, Database issue, D563-D569; doi:10.1093/nar/gkp871
Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Corrêa, Stefan A. Rensing, Birgit Kersten and Bernd Mueller-Roeber (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research, vol. 38, Database issue, D822-D827; doi:10.1093/nar/gkp805
Tags: bioinformatics, database, nar, nucleic acids research, transcription
