SynthesisPlant physiology2006
Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis.
Synthesis in Plant physiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed, 79 citations in OpenAlex.
- INDUCER OF CBF EXPRESSION 1 promotes cold-enhanced immunity by directly activating salicylic acid signaling.The Plant cell · 2024Article
- A De Novo Transcriptome Analysis Identifies Cold-Responsive Genes in the Seeds ofBioMed research international · 2022Article
- Article
- Identification of genes from the ICE-CBF-COR pathway under cold stress inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2018Article
- Cross-talk between freezing response and signaling for regulatory transcriptions of MIR475b and its targets by miR475b promoter in Populus suaveolens.Scientific reports · 2016Article
- Transcriptional Analysis of Resistance to Low Temperatures in Bermudagrass Crown Tissues.PloS one · 2015Article
- Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms.PloS one · 2015Article
- Article
- Review
- Molecular and functional characterization of cold-responsive C-repeat binding factors from Brachypodium distachyon.BMC plant biology · 2014Article
- Transcriptome sequencing and identification of cold tolerance genes in hardy Corylus species (C. heterophylla Fisch) floral buds.PloS one · 2014Article
- Regulatory role of membrane fluidity in gene expression and physiological functions.Photosynthesis research · 2013Review
- Role of CBFs as integrators of chloroplast redox, phytochrome and plant hormone signaling during cold acclimation.International journal of molecular sciences · 2013Review
- Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice Jumli Marshi.PloS one · 2013Article
- Article
- Spaceflight transcriptomes: unique responses to a novel environment.Astrobiology · 2012Article
- CsICE1 and CsCBF1: two transcription factors involved in cold responses in Camellia sinensis.Plant cell reports · 2012Article
- Male gametophyte-specific WRKY34 transcription factor mediates cold sensitivity of mature pollen in Arabidopsis.Journal of experimental botany · 2010Article
- Low temperatures impact dormancy status, flowering competence, and transcript profiles in crown buds of leafy spurge.Plant molecular biology · 2010Article
- Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice.BMC plant biology · 2009Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (-1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.