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Tytuł:
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OrthReg: a tool to predict cis -regulatory elements based on cross-species orthologous sequence conservation.
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Autorzy:
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Ma YF; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Huang CP; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Lu FR; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Li JX; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, Yunnan 650091, China.; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China.
Han XM; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Adeola AC; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Gao Y; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Deng JK; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Xie HB; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail: .
Zhang YP; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail: .
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Źródło:
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Zoological research [Zool Res] 2020 Jul 18; Vol. 41 (4), pp. 471-475.
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Typ publikacji:
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Letter; Validation Study
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Język:
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English
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Imprint Name(s):
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Original Publication: Beijing, China : Science Press, 2016-
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MeSH Terms:
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Base Sequence*
Conserved Sequence*
Genome*
Genome-Wide Association Study/*methods
Mice/*genetics
Sus scrofa/*genetics
Animals ; Genome-Wide Association Study/veterinary ; Humans
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References:
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Contributed Indexing:
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Keywords: Cis-regulatory element prediction; Comparative genomics; Conserved noncoding sequence
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Entry Date(s):
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Date Created: 20200617 Date Completed: 20201216 Latest Revision: 20201216
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Update Code:
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20240105
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PubMed Central ID:
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PMC7340522
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DOI:
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10.24272/j.issn.2095-8137.2020.099
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PMID:
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32543792
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Cis -regulatory elements play an important role in the development of traits and disease in organisms (Ma et al., 2020; Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements (ENCODE) (Davis et al., 2018) and Functional Annotation of Animal Genomes (FAANG) (FAANG Consortium et al., 2015) offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms. In this study, we developed a tool (OrthReg) for annotating conserved orthologous cis -regulatory elements in targeted genomes using an annotated reference genome. Cross-species validation of this annotation tool using human and mouse ENCODE data confirmed the robustness of this strategy. To explore the efficiency of the tool, we annotated the pig genome and identified more than 28 million regulatory annotation records using the reference human ENCODE data. With this regulatory annotation, some putative regulatory non-coding variants were identified within domestication sweeps in European and East Asian pigs. Thus, this tool can utilize data produced by ENCODE, FAANG, and similar projects, and can be easily extended to customized experimental data. The extensive application of this tool will help to identify informative single nucleotide polymorphisms (SNPs) in post-genome-wide association studies and resequencing analysis of organisms with limited regulatory annotation data.
