ATTED-II provides coexpressed gene networks for Arabidopsis

By T. Obayashi, Shinpei Hayashi, M. Saeki, H. Ohta, Kengo Kinoshita. Nucleic Acids Res., 2008

383 citations recorded by the source corpus.

ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein–protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/57cec49daa0e6f87a4aa3934a2fda9c7ec08d882

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Citations in the corpus

• PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update (2009, background): “The protein summary page now provides dynamic links to further external resources, such as Aramemnon (18), eFP browser (19), co-expression networks ATTED-II (20), subcellular localization (21) and other more general protein information at the GABI Primary Database (22).”
• Regulation of Photosynthesis during Abiotic Stress-Induced Photoinhibition. (2015, background): “Studies on 236 TAP38/PPH1 have indicated that PPH1 may have other unknown function(s) besides STN7-237 mediated dephosphorylation of LHCII, as co-expression of PPH1 and STN7 was not detected 238 (Nath et al., 2013a; Obayashi et al., 2009).”
• Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “ATTED database analysis of transcriptional coregulation (atted.jp/data/cor/At1g25290.html; Obayashi et al., 2009) with RBL10 (At1g25290) identifies two chloroplast proteins: EGY2, a S2P-like putative membrane-located metalloprotease; and CRR1 (chlororespiration reduction 1), a dihydrodipicolinate re”
• AGRIS: the Arabidopsis Gene Regulatory Information Server, an update (2010, background): “Different from other community resources such as ATTED-II, which focuses primarily on co-expression analysis (4), Athena that focuses on promoter analysis (5) or PlnTFDB (6), which harbors computationally curated information on TF from many different plant species, AGRIS is Arabidopsis–centered, pri”