ArticlePloS one2012
Discovery of stress responsive DNA regulatory motifs in Arabidopsis.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites inGenes · 2023Article
- TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes.BMC plant biology · 2022Article
- Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation.The Plant cell · 2018Article
- Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes.Frontiers in plant science · 2018Article
- W-box and G-box elements play important roles in early senescence of rice flag leaf.Scientific reports · 2016Article
- Emerging tools, concepts and ideas to track the modulator genes underlying plant drought adaptive traits: An overview.Plant signaling & behavior · 2016Review
- Salt stress and senescence: identification of cross-talk regulatory components.Journal of experimental botany · 2014Article
- 'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences.Database : the journal of biological databases and curation · 2014Article
- Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library.BMC plant biology · 2013Article
- Juvenile hormone and its receptor, methoprene-tolerant, control the dynamics of mosquito gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways.PLoS genetics · 2013Article
- Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk.Frontiers in plant science · 2012Article
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Authors and funding
6 authors.
Funding
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Abstract
The discovery of DNA regulatory motifs in the sequenced genomes using computational methods remains challenging. Here, we present MotifIndexer--a comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level. Using word-counting methods, we indexed the existence of every 8-mer oligo composed of bases A, C, G, T, r, y, s, w, m, k, n or 12-mer oligo composed of A, C, G, T, n, in the promoters of all predicted genes of Arabidopsis thaliana genome and of selected stress-induced co-expressed genes. From this analysis, we identified number of over-represented motifs. Among these, major critical motifs were identified using a position filter. We used a model based on uniform distribution and the z-scores derived from this model to describe position bias. Interestingly, many motifs showed position bias towards the transcription start site. We extended this model to show biased distribution of motifs in the genomes of both A. thaliana and rice. We also used MotifIndexer to identify conserved motifs in co-expressed gene groups from two Arabidopsis species, A. thaliana and A. lyrata. This new comparative genomics method does not depend on alignments of homologous gene promoter sequences.
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