RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice.

Abstract:

:Microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. However, there have been no reports, to date, of such a database being constructed for rice (Oryza sativa). Here, we describe the construction of such a database, called RiceArrayNet (RAN; http://www.ggbio.com/arraynet/), which provides information on coexpression between genes in terms of correlation coefficients (r values). The average number of coexpressed genes is 214, with sd of 440 at r >or= 0.5. Given the correlation between genes in a gene pair, the degrees of closeness between genes can be visualized in a relational tree and a relational network. The distribution of correlated genes according to degree of stringency shows how each gene is related to other genes. As an application of RAN, the 16-member L7Ae ribosomal protein family was explored for coexpressed genes and gene expression values within and between rice and Arabidopsis (Arabidopsis thaliana), and common and unique features in coexpression partners and expression patterns were observed for these family members. We observed a correlation pattern between Os01g0968800, a drought-responsive element-binding transcription factor, Os02g0790500, a trehalose-6-phosphate synthase, and Os06g0219500, a small heat shock factor, reflecting the fact that genes responding to the same biological stresses are regulated together. The RAN database can be used as a tool to gain insight into a particular gene by examining its coexpression partners.

journal_name

Plant Physiol

journal_title

Plant physiology

authors

Lee TH,Kim YK,Pham TT,Song SI,Kim JK,Kang KY,An G,Jung KH,Galbraith DW,Kim M,Yoon UH,Nahm BH

doi

10.1104/pp.109.139030

subject

Has Abstract

pub_date

2009-09-01 00:00:00

pages

16-33

issue

1

eissn

0032-0889

issn

1532-2548

pii

pp.109.139030

journal_volume

151

pub_type

杂志文章
  • Adaptations of Photosynthetic Electron Transport, Carbon Assimilation, and Carbon Partitioning in Transgenic Nicotiana plumbaginifolia Plants to Changes in Nitrate Reductase Activity.

    abstract::Transgenic Nicotiana plumbaginifolia plants that express either a 5-fold increase or a 20-fold decrease in nitrate reductase (NR) activity were used to study the relationships between carbon and nitrogen metabolism in leaves. Under saturating irradiance the maximum rate of photosynthesis, per unit surface area, was de...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.104.1.171

    authors: Foyer CH,Lescure JC,Lefebvre C,Morot-Gaudry JF,Vincentz M,Vaucheret H

    更新日期:1994-01-01 00:00:00

  • A New UV-A/B Protecting Pigment in the Terrestrial Cyanobacterium Nostoc commune.

    abstract::A new ultraviolet (UV)-A/B absorbing pigment with maxima at 312 and 330 nanometers from the cosmopolitan terrestrial cyanobacterium Nostoc commune is described. The pigment is found in high amounts (up to 10% of dry weight) in colonies grown under solar UV radiation but only in low concentrations in laboratory culture...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.88.4.1055

    authors: Scherer S,Chen TW,Böger P

    更新日期:1988-12-01 00:00:00

  • Nucleoside Diphosphate Levels in Taproots and Fibrous Roots of Beta vulgaris L. : Implifications for Control of Sucrose Allocation between Two Sinks.

    abstract::Sucrose synthase (EC 2.4.1.13) of sugarbeet (Beta vulgaris L.) fibrous roots has a distinctly different order of preference for nucleoside diphosphate substrates than that of the taproot enzyme (Silvius, Snyder 1979 Plant Physiol 64: 1070-1073). Separation and quantitation of UDP, ADP, and GDP in root extracts by high...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.70.1.316

    authors: Silvius JE,Snyder FW,Kremer DF

    更新日期:1982-07-01 00:00:00

  • Purification and partial characterization of a membrane-associated lipoxygenase in tomato fruit.

    abstract::Membrane-associated lipoxygenase from green tomato (Lycopersicon esculentum L. cv Caruso) fruit has been purified 49-fold to a specific activity of 8.3 mumol.min(-1).mg(-1) of protein by solubilization of microsomal membranes with Triton X-100, followed by anion- exchange and size-exclusion chromatography. The apparen...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.100.4.1802

    authors: Bowsher CG,Ferrie BJ,Ghosh S,Todd J,Thompson JE,Rothstein SJ

    更新日期:1992-12-01 00:00:00

  • Diurnal trends in net photosynthetic rate and carbohydrate levels of soybean leaves.

    abstract::A study was made of diurnal trends in net photosynthetic rate and carbohydrate levels of unifoliolate leaves of soybean (Glycine max L. Merrill) under constant environmental conditions (50,000-lux light intensity, 24.5 C air temperature, 60% relative humidity, and 300 microliters of CO(2) per liter of air).Net photosy...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.51.5.871

    authors: Upmeyer DJ,Koller HR

    更新日期:1973-05-01 00:00:00

  • The DEK1 Calpain Linker Functions in Three-Dimensional Body Patterning in Physcomitrella patens.

    abstract::The DEFECTIVE KERNEL1 (DEK1) calpain is a conserved 240-kD key regulator of three-dimensional body patterning in land plants acting via mitotic cell plane positioning. The activity of the cytosolic C-terminal calpain protease is regulated by the membrane-anchored DEK1 MEM, which is connected to the calpain via the 600...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.16.00925

    authors: Johansen W,Ako AE,Demko V,Perroud PF,Rensing SA,Mekhlif AK,Olsen OA

    更新日期:2016-10-01 00:00:00

  • Differences in PpAAT1 Activity in High- and Low-Aroma Peach Varieties Affect γ-Decalactone Production.

    abstract::Aroma contributes to the unique flavors of fruits and is important for fruit quality evaluation. Among the many volatiles in peach (Prunus persica) fruits, γ-decalactone has the greatest contribution to the characteristic peach aroma. Some peach cultivars have γ-decalactone contents that are too low to detect. Compari...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.19.00964

    authors: Peng B,Yu M,Zhang B,Xu J,Ma R

    更新日期:2020-04-01 00:00:00

  • Wheat vegetative nitrogen compositional changes in response to reduced reproductive sink strength.

    abstract::N redistribution patterns and the N composition of vegetative tissues above the peduncle node of wheat (Triticum aestivum L.) plants with altered reproductive sink strength were evaluated to determine the role of vegetative storage proteins in the temporary storage of excess N destined for export. The degree of leaf s...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.99.4.1469

    authors: Mackown CT,Van Sanford DA,Zhang N

    更新日期:1992-08-01 00:00:00

  • Inactivation of maize phosphoenolpyruvate carboxylase by urea.

    abstract::Phosphoenolpyruvate carboxylase purified from leaves of maize (Zea mays, L.) is sensitive to the presence of urea. Exposure to 2.5 m urea for 30 min completely inactivates the enzyme, whereas for a concentration of 1.5 m urea, about 1 h is required. Malate appears to have no effect on inactivation by urea of phosphoen...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.100.3.1366

    authors: Wedding RT,Dole P,Chardot TP,Wu MX

    更新日期:1992-11-01 00:00:00

  • Ozone-induced Loss of Intracellular Potassium Ion from Chlorella sorokiniana.

    abstract::The unicellular algae Chlorella sorokiniana was used as a model system to investigate the interaction of ozone with plant cell membranes. Ozone induces K(+) leakage from Chlorella sorokiniana similar to the electrolytic loss observed from many higher plants under stressful conditions. The kinetics of this leakage indi...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.56.6.723

    authors: Chimiklis PE,Heath RL

    更新日期:1975-12-01 00:00:00

  • Identification and gene expression of anaerobically induced enolase in Echinochloa phyllopogon and Echinochloa crus-pavonis.

    abstract::Enolase (2-phospho-D-glycerate hydrolase, EC 4.2.1.11) has been identified as an anaerobic stress protein in Echinochloa oryzoides based on the homology of its internal amino acid sequence with those of enolases from other organisms, by immunological reactivity, and induction of catalytic activity during anaerobic str...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.2.433

    authors: Fox TC,Mujer CV,Andrews DL,Williams AS,Cobb BG,Kennedy RA,Rumpho ME

    更新日期:1995-10-01 00:00:00

  • A Cobalt Requirement for Symbiotic Growth of Azolla filiculoides in the Absence of Combined Nitrogen.

    abstract::Cobalt was shown to be essential for the symbiotic growth of Azolla filiculoides and Anabacna azollac in the absence of fixed nitrogen. Addition of 0.01 mug/liter cobalt resulted in large increases in yield, chlorophyll content and nitrogen fixation as compared to control cultures without cobalt. Cobalt was not requir...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.41.5.852

    authors: Johnson GV,Mayeux PA,Evans HJ

    更新日期:1966-05-01 00:00:00

  • Changes in indoleacetic Acid oxidase isoenzymes in tobacco tissues after treatment with 2,4-dichlorophenoxyacetic Acid.

    abstract::2,4-Dichlorophenoxyacetic acid had a multiple effect on the development of indoleacetic acid oxidase isoenzymes in tobacco callus tissues (Nicotiana tabacum, cv. White Gold) cultured in vitro, and the development of these isoenzymes was differentially associated with growth promotion or inhibition depending on the con...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.49.6.957

    authors: Lee TT

    更新日期:1972-06-01 00:00:00

  • Specific reduction of wheat storage proteins by thioredoxin h.

    abstract::Gliadins and glutenins, the major storage proteins of wheat endosperm (Triticum durum, Desf. cv Monroe), were reduced in vitro by the NADP/thioredoxin system (NADPH, NADP-thioredoxin reductase and thioredoxin; in plants, the h type) from either the same source or the bacterium Escherichia coli. A more limited reducti...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.99.3.919

    authors: Kobrehel K,Wong JH,Balogh A,Kiss F,Yee BC,Buchanan BB

    更新日期:1992-07-01 00:00:00

  • Saponin biosynthesis in Saponaria vaccaria. cDNAs encoding beta-amyrin synthase and a triterpene carboxylic acid glucosyltransferase.

    abstract::Saponaria vaccaria (Caryophyllaceae), a soapwort, known in western Canada as cowcockle, contains bioactive oleanane-type saponins similar to those found in soapbark tree (Quillaja saponaria; Rosaceae). To improve our understanding of the biosynthesis of these saponins, a combined polymerase chain reaction and expresse...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.106.088484

    authors: Meesapyodsuk D,Balsevich J,Reed DW,Covello PS

    更新日期:2007-02-01 00:00:00

  • The interplay of light and the circadian clock. Independent dual regulation of clock-controlled gene ccg-2(eas).

    abstract::Ambient light is the major agent mediating entrainment of circadian rhythms and is also a major factor influencing development and morphogenesis. We show that in Neurospora crassa the expression of clock-controlled gene 2 (ccg-2), a gene under the control of the circadian clock and allelic to the developmental gene ea...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.102.4.1299

    authors: Arpaia G,Loros JJ,Dunlap JC,Morelli G,Macino G

    更新日期:1993-08-01 00:00:00

  • Ovule abortion in Arabidopsis triggered by stress.

    abstract::Environmental stresses frequently decrease plant fertility. In Arabidopsis, the effect of salt stress on reproduction was examined using plants grown in hydroponic medium. Salt stress inhibited microsporogenesis and stamen filament elongation. Because plants grown in hydroponic media can be rapidly and transiently str...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.104.043091

    authors: Sun K,Hunt K,Hauser BA

    更新日期:2004-08-01 00:00:00

  • Metabolic Interactions between Spinach Leaf Nitrite Reductase and Ferredoxin-NADP Reductase: Competition for Reduced Ferredoxin.

    abstract::Steady state rates of NADP reduction decline upon commencement of nitrite reduction in reconstituted chloroplast preparations. Similarly, steady state rates of nitrite reduction are lower, but not zero, during concurrent NADP reduction. These results imply that competition for substrate occurs and suggest that nitrite...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.77.2.318

    authors: Baysdorfer C,Robinson JM

    更新日期:1985-02-01 00:00:00

  • Differential Effects of a Substituted Pyridazinone, BASF 13-338, on Pathways of Monogalactosyldiacylglycerol Synthesis in Arabidopsis.

    abstract::We have examined the effects of the substituted pyridazinone herbicide, 4-chloro-5-(dimethylamino)-2-phenyl-3(2H)pyridazinone (BASF 13-338, Sandoz 9785), on the desaturation of linoleic acid (18:2) on different molecular species of monogalactosyldiacylglycerol (MGDG) and phosphatidylcholine (PC) in leaf tissue of Arab...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.85.3.684

    authors: Norman HA,John JB

    更新日期:1987-11-01 00:00:00

  • Water Permeability during Tomato Fruit Development in Normal and rin Nonripening Mutant.

    abstract::This work tested one aspect of the relations between membrane permeability and fruit ripening. Membrane permeability was measured as [(3)H]water efflux rate from preloaded fruit pericarp disks. Different stages of fruit development were compared between two tomato (Lycopersicon esculentum Mill) strains: the normal Rut...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.56.6.813

    authors: Poovaiah BW,Mizrahi Y,Dostal HC,Cherry JH,Leopold AC

    更新日期:1975-12-01 00:00:00

  • Dormancy, Turion Formation, and Germination by Different Clones of Spirodela polyrrhiza.

    abstract::Some clones of Spirodela polyrrhiza form dormant bodies called turions which require several weeks of chilling treatment before they proceed to renew growth and develop into vegetative fronds. The individual fronds of Spirodela are less than 5 mm long and can be grown aseptically in liquid culture. Turion formation an...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.43.11.1866

    authors: Perry TO

    更新日期:1968-11-01 00:00:00

  • SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle.

    abstract::SHORT-ROOT (SHR) and SCARECROW (SCR) are required for stem cell maintenance in the Arabidopsis (Arabidopsis thaliana) root meristem, ensuring its indeterminate growth. Mutation of SHR and SCR genes results in disorganization of the quiescent center and loss of stem cell activity, resulting in the cessation of root gro...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.110.158857

    authors: Dhondt S,Coppens F,De Winter F,Swarup K,Merks RM,Inzé D,Bennett MJ,Beemster GT

    更新日期:2010-11-01 00:00:00

  • The effect of salt concentration on auxin stability in culture media.

    abstract::The concentrations of indole-3-acetic acid (IAA), naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) were followed for 35 days in cell-free liquid medium containing 100, 50, or 0% Murashige-Skoog (MS) salt base. Although the concentrations of NAA or 2,4-D remained constant the level of IAA decreas...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.81.3.934

    authors: Dunlap JR,Kresovich S,McGee RE

    更新日期:1986-07-01 00:00:00

  • Effect of glucose on the induction of nitrate reductase in corn roots.

    abstract::In Zea mays L., addition of glucose to the induction medium has no effect on the induction of nitrate reductase during the initial 3 hours either in root tips (0-10 mm) or mature root sections (25-35 mm). With longer times, higher levels of enzyme activity are recovered from both root segments when glucose is present ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.56.5.634

    authors: Aslam M,Oaks A

    更新日期:1975-11-01 00:00:00

  • The nuclear pore protein AtTPR is required for RNA homeostasis, flowering time, and auxin signaling.

    abstract::Nuclear pore complexes (NPCs) mediate the transport of RNA and other cargo between the nucleus and the cytoplasm. In vertebrates, the NPC protein TRANSLOCATED PROMOTER REGION (TPR) is associated with the inner filaments of the nuclear basket and is thought to serve as a scaffold for the assembly of transport machinery...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.107.100735

    authors: Jacob Y,Mongkolsiriwatana C,Veley KM,Kim SY,Michaels SD

    更新日期:2007-07-01 00:00:00

  • The high mannose oligosaccharide of phytohemagglutinin is attached to asparagine 12 and the modified oligosaccharide to asparagine 60.

    abstract::Phytohemagglutinin, the lectin of the common bean Phaseolus vulgaris, has a high mannose and a modified (fucosylated) oligosaccharide on each polypeptide. Fractionation by high performance liquid chromatography of tryptic digests of [(3)H]fucose or [(3)H]glucosamine labeled phytohemagglutinin, followed by amino acid s...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.81.1.320

    authors: Sturm A,Chrispeels MJ

    更新日期:1986-05-01 00:00:00

  • Messenger RNA-controlled Increase of Phenylalanine Ammonia-Lyase Activity in Parsley: Light-Independent Induction by Dilution of Cell Suspension Cultures into Water.

    abstract::A specific antiserum, raised against purified phenylalanine ammonialyase from irradiated cell suspension cultures of parsley (Petroselinum hortense Hoffm.), was used to compare the enzyme species induced either by dilution or by irradiation of the cell suspensions, to investigate the effect of dilution on the rate of ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.60.3.440

    authors: Schröder J,Betz B,Hahlbrock K

    更新日期:1977-09-01 00:00:00

  • The Role of Plastids in the Expression of Nuclear Genes for Thylakoid Proteins Studied with Chimeric [beta]-Glucuronidase Gene Fusions.

    abstract::We have analyzed plastid and nuclear gene expression in tobacco seedlings using the carotenoid biosynthesis inhibitor nor-flurazon. mRNA levels for three nuclear-encoded chlorophyll-binding proteins of photosystem I and photosystem II (CAB I and II and the CP 24 apoprotein) are no longer detectable in photobleached se...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.105.4.1355

    authors: Bolle C,Sopory S,Lubberstedt T,Klosgen RB,Herrmann RG,Oelmuller R

    更新日期:1994-08-01 00:00:00

  • Gibberellic Acid-Stimulated Arabidopsis6 Serves as an Integrator of Gibberellin, Abscisic Acid, and Glucose Signaling during Seed Germination in Arabidopsis.

    abstract::The DELLA protein REPRESSOR OF ga1-3-LIKE2 (RGL2) plays an important role in seed germination under different conditions through a number of transcription factors. However, the functions of the structural genes associated with RGL2-regulated germination are less defined. Here, we report the role of an Arabidopsis (Ara...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.15.00858

    authors: Zhong C,Xu H,Ye S,Wang S,Li L,Zhang S,Wang X

    更新日期:2015-11-01 00:00:00

  • Genetic and genomic evidence that sucrose is a global regulator of plant responses to phosphate starvation in Arabidopsis.

    abstract::Plants respond to phosphate (Pi) starvation by exhibiting a suite of developmental, biochemical, and physiological changes to cope with this nutritional stress. To understand the molecular mechanism underlying these responses, we isolated an Arabidopsis (Arabidopsis thaliana) mutant, hypersensitive to phosphate starva...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.110.171736

    authors: Lei M,Liu Y,Zhang B,Zhao Y,Wang X,Zhou Y,Raghothama KG,Liu D

    更新日期:2011-07-01 00:00:00