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Protocols

ATTED-II specifications

Information


Unique identifier OMICS_03264
Name ATTED-II
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 8.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Oryza sativa

Maintainer


  • person_outline Takeshi Obayashi

Publications for ATTED-II

ATTED-II citations

 (40)
library_books

Reduction of indole‐3‐acetic acid methyltransferase activity compensates for high‐temperature male sterility in Arabidopsis

2017
Plant Biotechnol J
PMCID: 5785359
PMID: 28574629
DOI: 10.1111/pbi.12768

[…] he Ohio State University, OH). Graphic heatmap representations were constructed using the Matrix2png website (Pavlidis and Noble, ). The first 30 genes co‐expressed with IAMT1 were retrieved from the ATTED‐II database (Aoki et al., ) and their expression values in flower organs (stage 12) obtained from AtGenExpress (Table ). Expression values in flower organs were normalized individually in all th […]

library_books

Skewing in Arabidopsis roots involves disparate environmental signaling pathways

2017
BMC Plant Biol
PMCID: 5286820
PMID: 28143395
DOI: 10.1186/s12870-017-0975-9

[…] ame magnitude, within ± 1 fold change (base 2 log scale). Heatmaps were generated using Gene-E (v. 3.0.204, Broad Institute, Cambridge, MA). Gene data was researched using g:Profiler [, ], agriGO [], ATTED-II [], Biogrid [, ], UniProt [], KEGG [, ], and STRING [] online databases. Additional visualization of gene networks was created using GeneMANIA [].For qRT-PCR validation of transcriptome micro […]

library_books

Recent Advances in Understanding the Molecular Mechanisms Regulating the Root System Response to Phosphate Deficiency in Arabidopsis

2016
Curr Genomics
PMCID: 4955032
PMID: 27499680
DOI: 10.2174/1389202917666160331201812

[…] ray Database [] and GENEVESTIGATOR []. These data sources can be combined with several meta-analysis tools using a guilt-by-association principle to help visualise correlated gene expression, such as ATTED-II [], and CressExpress []. The functional annotations in the gene's co-expression neighbourhood can then be used to hypothesise a biologically relevant relationship. Using ATTED ver7.1 (http:// […]

call_split

Survival trade offs in plant roots during colonization by closely related beneficial and pathogenic fungi

2016
Nat Commun
PMCID: 4859067
PMID: 27150427
DOI: 10.1038/ncomms11362
call_split See protocol

[…] ing the hypergeometric test and Bonferroni step-down corrected P values are represented. Co-regulated genes that were also co-expressed in other Arabidopsis expression data sets were identified using ATTED-II (http://atted.jp/) and co-expression networks were generated using Cytoscape (version 3.1.1). […]

library_books

Learning from Co expression Networks: Possibilities and Challenges

2016
Front Plant Sci
PMCID: 4825623
PMID: 27092161
DOI: 10.3389/fpls.2016.00444

[…] iewed in Brady and Provart, ; Usadel et al., ; Table ). These databases provide user-friendly interfaces to facilitate access to the data and most of them also offer integrated data processing tools. ATTED-II (Obayashi et al., , ) allows condition specific searches for co-expressed genes in several plant species. For Arabidopsis, CressExpress (Srinivasasainagendra et al., ) in addition allows sele […]

library_books

The Arabidopsis Domain of Unknown Function 1218 (DUF1218) Containing Proteins, MODIFYING WALL LIGNIN 1 and 2 (At1g31720/MWL 1 and At4g19370/MWL 2) Function Redundantly to Alter Secondary Cell Wall Lignin Content

2016
PLoS One
PMCID: 4773003
PMID: 26930070
DOI: 10.1371/journal.pone.0150254

[…] fferent developmental stages, was extracted from The Bio-Analytic Resource for Plant Biology (http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi) []. Co-expressed genes for MWL-1 and MWL-2 were queried on ATTED-II ( and Tables, respectively), while Gene Ontology-Full was performed using BiNGO 2.44 [] in Cytoscape 2.8.2 []. Finally, overrepresentation summary enrichment was performed with the REVIGO se […]


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ATTED-II institution(s)
Graduate School of Information Sciences, Tohoku University, Aoba-ku, Sendai, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
ATTED-II funding source(s)
This research was supported by the Japan Science and Technology Agency (CREST research project grant No. 11102558); Grants-in-Aid for Innovative Areas (grant No. 24114005), Scientific Research (grant Nos. 15K20863 and 15K18464) and Publication of Scientific Research Results (grant No. 15HP8044).

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