Abstract：
:MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 different data sets that include six human cell-types and 10 distinct mouse cell/tissues. The updated MPromDb version consists of computationally predicted (novel) and known active RNAP-II promoters (42,893 human and 48,366 mouse promoters) from various data sets freely available at NCBI GEO database. We found that 36% and 40% of protein-coding genes have alternative promoters in human and mouse genomes and ∼40% of promoters are tissue/cell specific. The identified RNAP-II promoters were annotated using various known and novel gene models. Additionally, for novel promoters we looked into other evidences-GenBank mRNAs, spliced ESTs, CAGE promoter tags and mRNA-seq reads. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. We have also integrated GBrowse genome browser with MPromDb for visualization of ChIP-seq profiles and to display the annotations. The current release of MPromDb can be accessed at http://bioinformatics.wistar.upenn.edu/MPromDb/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gupta R,Bhattacharyya A,Agosto-Perez FJ,Wickramasinghe P,Davuluri RVdoi
10.1093/nar/gkq1171subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D92-7issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq1171journal_volume
39pub_type
杂志文章abstract：:The gene for the small subunit of human calcium-activated neutral protease was isolated and sequenced. It is 11 kb long and comprises 11 exons. No TATA or CAT box was found upstream of the possible transcription initiation sites, but there are three so-called G-C box sequences and one G-C box-like sequence, which are ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.22.8805
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journal_title：Nucleic acids research
pub_type： 杂志文章
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf534
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.17.4055
更新日期：1993-08-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.8.1933
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.2.203
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.11.2207
更新日期：2000-06-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.21.4895
更新日期：1998-11-01 00:00:00
abstract：:As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...
journal_title：Nucleic acids research
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journal_title：Nucleic acids research
pub_type： 杂志文章,评审
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更新日期：1998-12-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw644
更新日期：2016-09-06 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg138
更新日期：2003-01-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part1.175
更新日期：1984-01-11 00:00:00
abstract：:DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl355
更新日期：2006-05-24 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv223
更新日期：2015-04-30 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.6.1473
更新日期：1976-06-01 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
abstract：:We have determined the nucleotide sequences of long terminal repeat (LTR) regions of Syrian hamster intracisternal A particle (IAP) genes. The size of the LTRs was 350 base-pairs (bp) and 376 bp in two clones, H10 and H18, respectively. Two LTRs at both ends of the IAP gene were linked to directly repeating 6 bp hamst...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.20.7169
更新日期：1983-10-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq912
更新日期：2011-01-01 00:00:00
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
pub_type： 杂志文章
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journal_title：Nucleic acids research
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更新日期：1998-06-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2003-02-01 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：2017-05-05 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx915
更新日期：2017-12-01 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：2016-01-04 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1173
更新日期：2010-04-01 00:00:00
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pub_type： 杂志文章
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更新日期：2001-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.8.1873
更新日期：1980-04-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.6.2431
更新日期：1988-03-25 00:00:00
