Japanese
Menu

Database Record

Thumbnail

ATTED-II: Arabidopsis thaliana trans-factor and cis-element prediction database

IDNBDC common database IDs, which should be written in parentheses if there are multiple titles, such as Japanese and English. NBDC00374
Database nameName of the database ATTED-II
Alternative nameAlternative name of the database Arabidopsis thaliana trans-factor and cis-element prediction database
URLURL of the database http://atted.jp/
Database maintenance siteSite maintaining the database Tohoku University (Link to J-Global), The University of Tokyo The Institute of Medical Science Human Genome Center (Link to J-Global)
Country/RegionCountry or region name where the database maintenance site is located Japan
Database descriptionDatabase descirption ATTED-II is a coexpression database for Arabidopsis and other plant species. It stores calculated coexpression data based on microarray data and RNAseq data from AtGenExpress (TAIR), ArrayExpress and DDBJ. Mutual rank (MR) index is used as a coexpression measure, shows a higher predictive power for gene function than the Pearson’s correlation coefficient (PCC). ATTED-II provides a list of coexpressed genes and their orthologous for a query gene. NetworkDrawer tool provides drawing of gene networks in multiple query genes. The coexpression data are downloadable from Bulk download page.
Organism(s) coveredNCBI Taxonomy names and IDs covered by the database Arabidopsis thaliana (3702), Oryza sativa (4530), Glycine max (3847), Zea mays (4577), Solanum lycopersicum (4081), Brassica rapa (3711), Vitis vinifera (29760), Populus trichocarpa (3694), Medicago truncatula (3880)
Tag - TargetTag to indicate targets for this database such as genome and protein
Genome/Gene
cDNA/EST
Genetic variation
Epigenetics
DNA
RNA
Protein
Carbohydrate
Lipid
Metabolite
Chemical compound
Drug
Cell/Organelle
Organism
Health/Disease
Tag - Information typeTag to indicate information types for this database such as sequence and structure
Phenotype
Bioresource
Method
Ontology/Terminology/Nomenclature
Environment
Sequence
3D structure
Chemical structure
Expression
Localization
Geographic Distribution
Interaction/Pathway
Taxonomy
Classification
Image/Movie
Bibliography/Documents
Portal
Repository
Reference(s) - PubMed ID/DOIPubMed IDs/DOI for papers related to the database
PubMed ID:29216398
DOI:-
PubMed ID:26546318
DOI:-
PubMed ID:24334350
DOI:-
PubMed ID:21217125
DOI:-
PubMed ID:18953027
DOI:-
PubMed ID:17130150
DOI:-
Language(s)Languages in which the contents of the database are displayed English
Operational statusOperational status for the database Active
Link(s) to Downloadable dataLinks to downloadable data http://atted.jp/top_download.shtml
Link(s) to MetaData of downloadable dataLinks to metadata of downloadable data http://atted.jp/download.shtml
Link(s) to Terms of useLinks to terms of use of downloadable data http://atted.jp/license.shtml
Link(s) to "How to use" ―
Contact information of database ―
Link(s) to API / SPARQL endpoint ―
Link to LSDB ArchiveLink to LSDB Archive ―
Link to MEDALS Database listLink to MEDALS Database list http://medals.jp/elist/detail/126.html
Link to TogoTVLink to TogoTV ―
Link to FAIRsharingLink to FAIRsharing https://fairsharing.org/biodbcore-000211
Similar databasesDatabases that are similar to this database.
Record maintainerRecord maintainer Integbio Database Catalog
Record sourceOrganization that originally created the record
Date of creation of this recordDate of creation of this English record 2013-06-17
Last update date of this recordLast update date of this English record 2019-02-04
Record license Creative Commons CC0 license