Abstract：
:Regulation of gene expression influences almost all biological processes in an organism; sequence-specific DNA-binding transcription factors are critical to this control. For most genomes, the repertoire of transcription factors is only partially known. Hitherto transcription factor identification has been largely based on genome annotation pipelines that use pairwise sequence comparisons, which detect only those factors similar to known genes, or on functional classification schemes that amalgamate many types of proteins into the category of 'transcription factor'. Using a novel transcription factor identification method, the DBD transcription factor database fills this void, providing genome-wide transcription factor predictions for organisms from across the tree of life. The prediction method behind DBD identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains. Thus, it is limited to factors that are homologus to those HMMs. The collection of HMMs is taken from two existing databases (Pfam and SUPERFAMILY), and is limited to models that exclusively detect transcription factors that specifically recognize DNA sequences. It does not include basal transcription factors or chromatin-associated proteins, for instance. Based on comparison with experimentally verified annotation, the prediction procedure is between 95% and 99% accurate. Between one quarter and one-half of our genome-wide predicted transcription factors represent previously uncharacterized proteins. The DBD (www.transcriptionfactor.org) consists of predicted transcription factor repertoires for 150 completely sequenced genomes, their domain assignments and the hand curated list of DNA-binding domain HMMs. Users can browse, search or download the predictions by genome, domain family or sequence identifier, view families of transcription factors based on domain architecture and receive predictions for a protein sequence.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kummerfeld SK,Teichmann SAdoi
10.1093/nar/gkj131keywords:
subject
Has Abstractpub_date
2006-01-01 00:00:00pages
D74-81issue
Database issueeissn
0305-1048issn
1362-4962pii
34/suppl_1/D74journal_volume
34pub_type
杂志文章abstract：:Thermal elution poly(U)-Sepharose chromatography was utilized to fractionate yeast mRNA based on poly(A) size. Analysis of the in vitro translation products of the fractionated RNAs in a wheat-embryo cell-free protein synthesis system shows a heterogeneous but equal distribution of these abundant translatable mRNAs in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3841
更新日期：1980-09-11 00:00:00
abstract：:With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorith...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1081
更新日期：2012-02-01 00:00:00
abstract：:DNA sequencing studies of two recently cloned human A gamma globin alleles has revealed a number of base differences which are clustered in the large intron (IVS-2). One allele has a previously undescribed IVS-2 sequence. Most of the allelic differences can be explained as resulting from a gene conversion event involv...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.11.4469
更新日期：1984-06-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.8.2369
更新日期：1979-12-20 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.20.4783
更新日期：1998-10-15 00:00:00
abstract：:Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility empl...
journal_title：Nucleic acids research
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doi：10.1093/nar/gkp037
更新日期：2009-04-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1364
更新日期：2013-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1163
更新日期：2015-01-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2014-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2011-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.22.9515
更新日期：1987-11-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.1.101
更新日期：1976-01-01 00:00:00
abstract：:Methylation of CpG motifs in DNA is involved in the control of gene expression and in several other epigenic effects. It suppresses also the immuno-stimulation properties of bacterial or viral DNAs that contain CPGS: However, effects of methylation on the DNA structure and dynamics are not clear. Here we carried out a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.11.2314
更新日期：2001-06-01 00:00:00
abstract：:DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx177
更新日期：2017-06-20 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa357
更新日期：2020-06-19 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa793
更新日期：2021-01-08 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq185
更新日期：2010-08-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.21.6597
更新日期：1982-11-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2013-08-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：1996-05-15 00:00:00
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journal_title：Nucleic acids research
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更新日期：2010-01-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2015-06-23 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1997-12-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1988-02-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2013-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2017-05-19 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2009-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2003-08-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.23.4864
更新日期：1995-12-11 00:00:00
abstract：:A new method is described for the direct construction of randomly mutagenized genes by applying the polymerase chain reaction (PCR) to an oligonucleotide synthesized using doped nucleotide reservoirs. We have demonstrated the utility of this method by generating a library of mutant HIV-1 tat genes. Several arbitrarily...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.20.5311
更新日期：1992-10-25 00:00:00
