| Name | ATTED II |
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| Aliases | Arabidopsis thaliana trans-factor and cis-element prediction database |
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| 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. |
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| Type | DB |
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| Main Institutes of management | Tohoku University | Human Genome Center (HGC), Institute of Medical Sciences, The University of Tokyo (IMSUT) |
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| Country of the Institute | Japan |
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| URL of the site | http://atted.jp/ |
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| Interface | GUI |
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| 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. |
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| Keyword | coexpressed gene | cis elements | microarray | TSS |
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| 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 |
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| External resources (databases) in building the product. | AtGenExpress |
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| Data type | Gene expression | microarray | Pathway |
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| Biological species in the main concern | Arabidopsis thaliana [Taxonomy_id: 3702, thale cress] |
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| Conditions of use | Attribution & Creative Commons |
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| Frequency of updates (in last two years) | 3 times / year |
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| Last date of updates (date of confirmation) | 2018/01/29 (2019/07/03) |
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| Main IDs used in the products | AGI code |
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| How to make a link to get access to each IDs. | http://atted.jp/data/cor/[AGI code].html |
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| 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) |
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| Published papers (PubMed IDs) | pmid:18953027 | pmid:17130150 | pmid:19767600 | pmid:19620096 | pmid:17932064 |
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| Operational Status | available |
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