Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

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doi:10.1093/nar/gkab951

Cited by 495 publications

(197 citation statements)

References 47 publications

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“…The assembled chloroplast genome of these 10 species was then uploaded to NCBI ( Table S3 ). The chloroplast genome of C. illinoinensis (cultivar Pawnee) was sequenced and assembled by our lab and can be downloaded by the accession GWHBGBH00000000 at National Genomics Data Center ( , accessed on 1 November 2021) [ 31 , 32 ].…”

Section: Methodsmentioning

confidence: 99%

Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

Luo

Chen

Guo

et al. 2021

Plants

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Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species’ chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.

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Section: Methodsmentioning

confidence: 99%

Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

Luo

Chen

Guo

et al. 2021

Plants

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“…To this end, valuable efforts have been made worldwide, with the purpose to develop several databases and tools in aid of EWAS data integration and analysis ( 7–12 ). In 2018, we, the EWAS team of the National Genomics Data Center (NGDC) ( 13 , 14 ), launched EWAS Atlas ( https://ngdc.cncb.ac.cn/ewas/atlas ), a EWAS knowledgebase hosting manually curated high-quality EWAS associations ( 15 ). Subsequently, we further constructed EWAS Data Hub ( https://ngdc.cncb.ac.cn/ewas/datahub ), a data portal for collecting and normalizing DNA methylation array data as well as archiving associated metadata ( 16 ).…”

Section: Introductionmentioning

confidence: 99%

EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study

Xiong

Yang

et al. 2021

Nucleic Acids Research

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Epigenome-Wide Association Study (EWAS) has become a standard strategy to discover DNA methylation variation of different phenotypes. Since 2018, we have developed EWAS Atlas and EWAS Data Hub to integrate a growing volume of EWAS knowledge and data, respectively. Here, we present EWAS Open Platform (https://ngdc.cncb.ac.cn/ewas) that includes EWAS Atlas, EWAS Data Hub and the newly developed EWAS Toolkit. In the current implementation, EWAS Open Platform integrates 617 018 high-quality EWAS associations from 910 publications, covering 51 phenotypes, 275 diseases and 104 environmental factors. It also provides well-normalized DNA methylation array data and the corresponding metadata from 115 852 samples, which involve 707 tissues, 218 cell lines and 528 diseases. Taking advantage of integrated knowledge and data in EWAS Atlas and EWAS Data Hub, EWAS Open Platform equips with EWAS Toolkit, a powerful one-stop site for EWAS enrichment, annotation, and knowledge network construction and visualization. Collectively, EWAS Open Platform provides open access to EWAS knowledge, data and toolkit and thus bears great utility for a broader range of relevant research.

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“…High-throughput circRNA sequencing and subsequent bioinformatics analysis were performed by CloudSeq Biotech (Shanghai, China) as follows. The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive ( Chen et al, 2021a ) in National Genomics Data Center ( Cncb-Ngdc, 2022 ), China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA-Human: HRA001908) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human . First, linear RNAs were removed from the total RNA in each sample after treatment with RNase-R (Epicenter, Madison, WI, United States).…”

Section: Methodsmentioning

confidence: 99%

Hsa_circ_0031608: A Potential Modulator of VSMC Phenotype in the Rupture of Intracranial Aneurysms

Wang

Luo

Tang

et al. 2022

Front. Mol. Neurosci.

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Background and PurposePhenotypic modulation of vascular smooth muscle cells (VSMCs) plays an important role in the development of intracranial aneurysms (IAs). Growing evidence has demonstrated that circular RNAs (circRNAs) may serve as a potential modulator of VSMC phenotype in various vascular diseases. This study aimed to assess the potential function of circRNAs in the rupture of IAs and VSMC phenotypic modulation.MethodsUsing surgically dissected human ruptured (n = 8) and unruptured (n = 8) IA lesions, differentially expressed circRNAs were screened by transcriptomic sequencing and verified using qRT-PCR. Based on the screened circRNA, we predicted and screened the combined miRNA and downstream mRNAs to construct circRNA-miRNA-mRNA networks. Further in vitro experiments were performed to investigate the relationship between the validated circRNA and the phenotypic switching of VSMCs.ResultsWe found 1,373 differentially expressed genes in ruptured versus unruptured aneurysms. The top five dysregulated circRNAs were selected for qRT-PCR validation. We found hsa_circ_0031608 was both highly expressed in ruptured IAs and pro-inflammatory transformation of VSMCs. Then, a regulatory circRNA-miRNA-mRNA with one circRNA node, six miRNA nodes, and 84 mRNA nodes was constructed. GO analysis and KEGG pathway enrichment analysis were performed on mRNAs in the network. Then, a PPI network was built based on these mRNAs and five hub genes were identified (FOXO3, DICER1, CCND2, IGF1R, and TNRC6B) by the cytoHubba plugin in Cytoscape software. In vitro, overexpression of hsa_circ_0031608 influenced the expression of VSMC phenotypic markers validated by qPCR and Western blotting. Furthermore, hsa_circ_0031608 promoted the migration and proliferation capacity of VSMCs.Conclusionhsa_circ_0031608 regulated the phenotypic modulation of VSMCs and played an important role in the rupture of IAs. The specific mechanism should be further studied and confirmed.

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Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

Cited by 495 publications

References 47 publications

Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study

Hsa_circ_0031608: A Potential Modulator of VSMC Phenotype in the Rupture of Intracranial Aneurysms

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