Obayashi T, Hibara H, Kagaya Y, Aoki Y, Kinoshita K.(2022)ATTED-II v11: a plant gene coexpression database using a sample balancing technique by subagging of principal components.Plant Cell Physiology,63, 869-881
<Previous References>
Obayashi T, Aoki Y, Tadaka S, Kagaya Y, Kinoshita K.(2018)ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of Statistical Property of the Mutual Rank Index.Plant Cell Physiology,59, e3
Aoki Y, Okamura Y, Tadaka S, Kinoshita K, Obayashi T.(2016)ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression.Plant Cell Physiology,57, e5
Obayashi T, Okamura Y, Ito S, Tadaka S, Aoki Y, Shirota M, Kinoshita K.(2014)ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants.Plant Cell Physiology,55, e6
Obayashi T, Nishida K, Kasahara K, Kinoshita K.(2011)ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.Plant Cell Physiology,52, 213-9
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K.(2009)ATTED-II provides coexpressed gene networks for Arabidopsis.Nucleic Acids Res.,37, D987-91.
Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H.(2007)ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.Nucleic Acids Res.,35, D863-9.
Technical papers to construct ATTED-II;
<Review with MR examples>Obayashi T, Kinoshita K.(2010)Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.J Plant Res.,123, 311-9.
<MR>Obayashi T, Kinoshita K.(2009)Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.DNA Res.,16, 249-60.
<Coex stability>Kinoshita K, Obayashi T.(2009)Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.Bioinformatics.,25. 2677-84.
Other related papers;
<Coexpression comparison>Okamura Y, Obayashi T, Kinoshita K.(2015)Comparison of gene coexpression profiles and construction of conserved gene networks to find functional modules.PLoS One,10. e0132039.
<Review of coexpression databases in plant>Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ.(2009)Coexpression Tools for Plant Biology: Opportunities for Hypothesis Generation and Caveats.Plant Cell and Environment,32. 1633-51.
<Coexpression database for mammals>Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K.(2008)COXPRESdb: a database of coexpressed gene networks in mammals.Nucleic Acids Res.,36. D77-82.
<Coexpression database for microalgae>Aoki Y, Okamura Y, Ohta H, Kinoshita K, Obayashi T.(2016)ALCOdb: Gene Coexpression Database for Microalgae.Plant Cell Physiol.,in press.
Examples to use coexpression data in ATTED-II to estimate biological functions of target genes with disruptant analyses
<Enzyme>Maeda H et al.(2011)Prephenate aminotransferase directs plant phenylalanine biosynthesis via arogenate.Nature Chemical Biology
<QTL>Jimenez-Gomez JM et al.(2010)Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis.PLoS Genet.
<Regulation>Long TA et al.(2010)The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.Plant Cell
<Regulation>Doniwa Y et al.(2010)The involvement of a PPR protein of the P subfamily in partial RNA editing of an Arabidopsis mitochondrial transcript.Gene
<Regulation>Sugano SS et al.(2010)Stomagen positively regulates stomatal density in Arabidopsis.Nature
<Enzyme>Sawada Y et al.(2009)Omics-based approaches to methionine side chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase.Plant Cell Physiology
<Transporter>Sawada Y et al.(2009)Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis.Plant Cell Physiology
<Enzyme>Okazaki Y et al.(2009)A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis.Plant Cell
<Enzyme>Bednarek K et al.(2009)A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense.Science
<Complex>Ishikawa N et al.(2008)NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis.Plant Cell Physiology
<Regulation>Yamada K et al.(2008)NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana.Plant Cell
<Complex>Takabayashi A et al.(2008)Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches.Plant J
<Enzyme>Yonekura-Sakakibara K et al.(2008)Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis.Plant Cell
<Complex>Takahashi N et al.(2008)The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1.EMBO J
<Complex>Ishihara S et al.(2007)Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis.Plant Physiology
<Enzyme>Yonekura-Sakakibara K et al.(2007)Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics.J Biol Chem
<Regulation>Hirai MY et al.(2007)Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis.Proc Natl Acad Sci USA
