DoOP Edit

Citations: 17

z-index: 1.21

Basic information
Short name DoOP
Full name Database of Orthologous Promoters
Description DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Based on the Arabidopsis thaliana and Homo sapiens genome annotation, the developers collected the orthologous promoter sequences from Viridiplantae and Chordata species.
URL http://doop.abc.hu/
Year founded 2005
Last update & version 2009-01-01 v3.0
Accessibility Accessible
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

University/Institution Agricultural Research Institute, Hungarian Academy of Sciences
Address Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Brunszvik u, 2, H-2462, Hungary
City
Province/State
Country/Region Hungary
Contact name (PI/Team) Endre Barta
Contact email (PI/Helpdesk) barta@abc.hu
Data information
Data object
Data type
Database category
Major organism
Keyword
Publications
  • DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes. [PMID: 19534755]
    Endre Sebestyén, Tibor Nagy, Sándor Suhai, Endre Barta

    The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). We have developed a new tool called DoOPSearch http://doopsearch.abc.hu for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes.

    BMC Bioinformatics 2009:10 Suppl 6()

    3 Citations (from Europe PMC, 2019-06-22)

  • DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. [PMID: 15608291]
    Endre Barta, Endre Sebestyén, Tamás B Pálfy, Gábor Tóth, Csaba P Ortutay, László Patthy

    DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21,061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.

    Nucleic Acids Res 2005:33(Database issue)

    14 Citations (from Europe PMC, 2019-06-22)

Rank

  • Ranking in all databases: No. 2895
  • Ranking in category/categories:
    • Phylogeny and homology: No. 118
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of DoOP.

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Record metadata

  • Created on: 2015-07-11
    • ***ina@***c.cn [2019-06-10]
    • ***ina@***c.cn [2018-06-14]
    • ***ina@***c.cn [2016-04-08]
    • ***gj@***c.cn [2016-04-04]
    • ***ina@***c.cn [2016-03-30]
    • ***engwei@***63.com [2016-02-07]
    • ***gj@***c.cn [2015-12-07]

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