ArticlePlants (Basel, Switzerland)2019
Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice.
Article in Plants (Basel, Switzerland), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 42 citations in OpenAlex.
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- Transcription factors in Orinus: novel insights into transcription regulation for speciation adaptation on the Qinghai-Xizang (Tibet) Plateau.BMC plant biology · 2025Article
- Comparative analysis of the LEA gene family in seven Ipomoea species, focuses on sweet potato (Ipomoea batatas L.).BMC plant biology · 2024Article
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- Genome-Wide Analysis of Aquaporins Gene Family inInternational journal of molecular sciences · 2024Article
- Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content.Plants (Basel, Switzerland) · 2024Article
- A Novel Repetition Frequency-Based DNA Encoding Scheme to Predict Human and Mouse DNA Enhancers with Deep Learning.Biomimetics (Basel, Switzerland) · 2023Article
- Comparative analysis of theFrontiers in plant science · 2023Article
- Genome-wide characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response.Frontiers in plant science · 2023Article
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- Genome-Wide Analysis of Type-III Polyketide Synthases in Wheat and Possible Roles in Wheat Sheath-Blight Resistance.International journal of molecular sciences · 2022Article
- Expression Profile of Sorghum Genes andPlants (Basel, Switzerland) · 2022Article
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- Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice.Scientific reports · 2021Article
- Genome-Wide Identification, Characterization and Expression Analysis of the JAZ Gene Family in Resistance to Gray Leaf Spots in Tomato.International journal of molecular sciences · 2021Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene's expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some-but not all-CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.
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