The Diurnal Project: Diurnal and Circadian Expression Profiling, Model-based Pattern Matching, and Promoter Analysis

Mockler, Todd C.; Michael, T. P.; Priest, Henry D.; Shen, Rongkun; Sullivan, Christopher; Givan, Scott A.; McEntee, Connor; Kay, Steve A.; Chory, Joanne

doi:10.1101/sqb.2007.72.006

Cited by 356 publications

(447 citation statements)

References 46 publications

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“…SPL7 expression cycles under continuous conditions and this oscillation is almost lost in the phyB mutant. 16 The presence of GTAC boxes, the cis-element recognized by the SPL7 transcription factor, 8 does not correlate with gene induction under Cu deficiency. 13 In addition to positional effects in promoter occupancy and other overlapping cis-regulatory elements, temporal factors could also affect dynamic changes in gene expression.…”

Section: Plasma Membrane High Affinity Copper Transport Is Under Lighmentioning

confidence: 99%

“…COPT2) is subjected to circadian regulation. 7 A high number of SPL7-dependent Cu-deficiency responsive genes 13 show cyclic expression, 16 peaking around 22 h with an expression phase only slightly behind the SPL7 oscillation (Fig. 1).…”

Section: Plasma Membrane High Affinity Copper Transport Is Under Lighmentioning

confidence: 99%

“…15 COPT1 has also been shown to exhibit a daily oscillation regulated by the circadian clock. 3 According to the DIURNAL database, 16 COPT1 expression peaks at 21.5 h, which is only several hours before the subsequent dawn. Furthermore, analysis of the COPT1, COPT2 and COPT6 promoter regions reveals multiple putative light and circadian cis-regulatory elements.…”

Section: Plasma Membrane High Affinity Copper Transport Is Under Lighmentioning

confidence: 99%

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Daily rhythmicity of high affinity copper transport

Perea-García

Sanz

Moreno

et al. 2016

Plant Signaling & Behavior

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Section: Plasma Membrane High Affinity Copper Transport Is Under Lighmentioning

confidence: 99%

Section: Plasma Membrane High Affinity Copper Transport Is Under Lighmentioning

confidence: 99%

Section: Plasma Membrane High Affinity Copper Transport Is Under Lighmentioning

confidence: 99%

See 1 more Smart Citation

Daily rhythmicity of high affinity copper transport

Perea-García

Sanz

Moreno

et al. 2016

Plant Signaling & Behavior

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“…Our analysis is based on four independent gene expression profiling experiments described in Mockler et al (2007), Edwards et al (2006) and Grzegorczyk et al (2008). In these studies, wild-type Col-0 seedlings of Arabidopsis thaliana were grown for 7 days under artificially controlled light-dark cycles.…”

Section: Arabidopsis Datamentioning

confidence: 99%

Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series

2011

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To understand the processes of growth and biomass production in plants, we ultimately need to elucidate the structure of the underlying regulatory networks at the molecular level. The advent of high-throughput postgenomic technologies has spurred substantial interest in reverse engineering these networks from data, and several techniques from machine learning and multivariate statistics have recently been proposed. The present article discusses the problem of inferring gene regulatory networks from gene expression time series, and we focus our exposition on the methodology of Bayesian networks. We describe dynamic Bayesian networks and explain their advantages over other statistical methods. We introduce a novel information sharing scheme, which allows us to infer gene regulatory networks from multiple sources of gene expression data more accurately. We illustrate and test this method on a set of synthetic data, using three different measures to quantify the network reconstruction accuracy. The main application of our method is related to the problem of circadian regulation in plants, where we aim to reconstruct the regulatory networks of nine circadian genes

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“…Development series (Schmid et al 2005), abiotic-stress series (Kilian et al 2007), light series, pathogen series and tiling array series (Laubinger et al 2008;Zeller et al 2009) microarray data were downloaded from the Weigel World web site (http://www.weigelworld.org/). Diurnal microarray data (Michael et al 2008;Mockler et al 2007) was downloaded from ArrayExpress (Accession Number: E-MEXP-1304, http:// www.ebi.ac.uk/arrayexpress/, Parkinson et al 2009). All other microarray data were downloaded from the AtGenExpressJPN web site (http://igrt0.psc.riken.jp/, Goda et al 2008).…”

Section: The Data and Software Implemented In Fioredbmentioning

confidence: 99%