Name ATTED II
Aliases Arabidopsis thaliana trans-factor and cis-element prediction database
Description

"ATTED-II provides predicted cis elements and co-regulated gene relationships in Arabidopsis thaliana to estimate gene functions. Data source of coexpressed genes is publicly available microarray data (58 experiments, 1388 slides) collected by AtGenExpress. Coexpression measure is mutual rank (MR) based on weighted Pearson's correlation coefficients. CoexSearch function is newly supplied as ""CoexSearch"" in Search menu at Mar 2010. NEDO project products are included in ATTEDⅡ."

Type DB
Main Institutes of management "TOHOKU UNIVERSITY and Human Genome Center, Institute of MedicalSciences, TOKYO UNIVERSITY"
Country of the Institute Japan
URL of the site http://atted.jp/
Interface GUI
Input example

"step1: Input the keyword "MYB2" in the text box on the upper side of the top page, push "Search" button.step2: Click the hyperlink "list" on the right side of search result table, and you can see the coexpressed gene."

Keyword
coexpressed gene | cis elements | microarray | TSS
Amount of the all data for download(Mbyte) | Method to obtain the all data. 50560|Donwload from the page http://atted.jp/top_download.shtml
External resources (databases) in building the product. AtGenExpress
Data type "Gene expression , microarray, Pathway"
Biological species in the main concern
"Arabidopsis thaliana [Taxonomy_id: 3702, thale cress]"
Conditions of use Attribution & Creative Commons
Frequency of updates (in last two years) 3 times / year
Last date of updates (date of confirmation) 2013/08/17 (2013/08/18)
Main IDs used in the products AGI code
How to make a link to get access to each IDs. http://atted.jp/data/cor/[AGI code].html
external databases to which this database/tool have links

EBI(http://www.ebi.ac.uk/QuickGO/) | KEGG(http://www.genome.jp/kegg/kegg2.html) | TAIR(http://arabidopsis.org/index.jsp) | RAP-DB(http://rapdb.dna.affrc.go.jp/) | SALAD Database(http://salad.dna.affrc.go.jp/salad/) | NCBI(http://www.ncbi.nlm.nih.gov/) | TIGER | MIPS(http://mips.helmholtz-muenchen.de/cgi-bin/proj/thal/search_gene) | SIGnAL(http://signal.salk.edu/) | Arabidopsis MPSS Plus(http://mpss.udel.edu/at/) | Arabidopsis eFP Browser(http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi) | AthaMap(http://www.athamap.de/index.php) | KATANA(http://www.kazusa.or.jp/katana/index.html) | TilViz(http://jsp.weigelworld.org/tileviz/tileviz.jsp)

Published papers (PubMed IDs)

pmid:18953027 | pmid:17130150 | pmid:19767600 | pmid:19620096 | pmid:17932064