ArticlePlant physiology2011
DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes.
Article in Plant physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 46 citations in OpenAlex.
- Article
- Transcriptome-based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae.Journal of microbiology (Seoul, Korea) · 2023Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Biological and Molecular Components for Genetically Engineering Biosensors in Plants.Biodesign research · 2022Article
- TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.Briefings in bioinformatics · 2021Article
- Article
- Article
- Natural Sequence Variations and Combinations of GNP1 and NAL1 Determine the Grain Number per Panicle in Rice.Rice (New York, N.Y.) · 2020Article
- Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters.PloS one · 2019Article
- Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.Scientific reports · 2018Article
- Article
- Article
- Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- TSSPlant: a new tool for prediction of plant Pol II promoters.Nucleic acids research · 2017Article
- DNA structural features of eukaryotic TATA-containing and TATA-less promoters.FEBS open bio · 2017Article
- Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties.Plant physiology · 2016Article
- Article
- Genetic and epigenetic determinants mediate proneness of oncogene breakpoint sites for involvement in TCR translocations.Genes and immunity · 2014Article
- A double SORLIP1 element is required for high light induction of ELIP genes in Arabidopsis thaliana.Plant molecular biology · 2014Article
- The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.Bioinformatics and biology insights · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.
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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.