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.
PMID:35353884
DOI:10.1093/pcp/pcac041
<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.
PMID:29216398
DOI:10.1093/pcp/pcx191
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.
PMID:26546318
DOI:10.1093/pcp/pcv165
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.
PMID:24334350
DOI:10.1093/pcp/pct178
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: 213-219.
PMID:21217125
DOI:10.1093/pcp/pcq203
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-D869.
PMID:17130150
DOI:10.1093/nar/gkl783
Other related papers
<Review>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: 311-319.
PMID:20383554
DOI:10.1007/s10265-010-0333-6
<Review>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: 1633-1651.
PMID:19712066
DOI:10.1111/j.1365-3040.2009.02040.x
<MR index>Obayashi T, Kinoshita K.(2009)Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.DNA Res.,16: 249-260.
PMID:19767600
DOI:10.1093/dnares/dsp016
<For mammals>Obayashi T, Kodate S, Hibara H, Kagaya Y, Kinoshita K.(2023)COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic Acids Res.,51: D80-87.
PMID:36350658
DOI:10.1093/nar/gkac983
<For microalgae>Aoki Y, Okamura Y, Ohta H, Kinoshita K, Obayashi T.(2016)ALCOdb: Gene Coexpression Database for Microalgae.Plant Cell Physiol.,57: e3.
PMID:26644461
DOI:10.1093/pcp/pcv190
<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.
PMID:26147120
DOI:10.1371/journal.pone.0132039
Examples to use coexpression data in ATTED-II to estimate biological functions of target genes with disruptant analyses
<Transporter> Temple H et al.(2022)Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation.Nat Plant
PMID:35681018
<Enzyme>Huang AC et al.(2019)A specialized metabolic network selectively modulates Arabidopsis root microbiota.Science
PMID:31073042
<Transporter>Saito H et al.(2015)The jasmonate-responsive GTR1 transporter is required for gibberellin-mediated stamen development in Arabidopsis.Nat Commun
PMID:25648767
<Enzyme>Ohgami S et al.(2015)Volatile Glycosylation in Tea Plants: Sequential Glycosylations for the Biosynthesis of Aroma b-Primeverosides Are Catalyzed by Two Camellia sinensis Glycosyltransferases.Plant Physiol
PMID:25922059
<Enzyme>Maeda H et al.(2011)Prephenate aminotransferase directs plant phenylalanine biosynthesis via arogenate.Nature Chemical Biology
PMID:21102469
<QTL>Jimenez-Gomez JM et al.(2010)Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis.PLoS Genet.
PMID:20838594
<Regulation>Long TA et al.(2010)The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.Plant Cell
PMID:20675571
<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
PMID:20010603
<Regulation>Sugano SS et al.(2010)Stomagen positively regulates stomatal density in Arabidopsis.Nature
PMID:20010603
<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
PMID:19493961
<Transporter>Sawada Y et al.(2009)Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis.Plant Cell Physiology
PMID:19633020
<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
PMID:19286968
<Enzyme>Bednarek K et al.(2009)A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense.Science
PMID:19095900
<Genetics>Kanno T et al.(2008)A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.Nat Genet
PMID:18425128
<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
PMID:18535009
<Regulation>Yamada K et al.(2008)NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana.Plant Cell
PMID:18780803
<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
PMID:18785996
<Enzyme>Yonekura-Sakakibara K et al.(2008)Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis.Plant Cell
PMID:18757557
<Complex>Takahashi N et al.(2008)The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1.EMBO J
PMID:18528439
<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
PMID:17827269
<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
PMID:17314094
<Regulation>Hirai MY et al.(2007)Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis.Proc Natl Acad Sci USA
PMID:17420480
