EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online

Chen, Tong; Zhang, Haiyan; Liu, Yu; Liu, Yongxin; Huang, Lu-Qi

doi:10.1016/j.jgg.2021.07.007

Cited by 247 publications

(146 citation statements)

References 17 publications

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“…Spearman correlation analysis was performed to explore the correlation between the PSI values of OS-ASEs and the expression levels of SF genes ( Bishara and Hittner, 2012 ). The correlation networks visualization was visualized by EVeen ( Chen T. et al, 2021 ) with SFs and the OS-ASEs as vertices and the Spearman significant correlation between them as edges. It is assumed that the value of a vertex in a network depends first on its position in the network.…”

Section: Methodsmentioning

confidence: 99%

Screening and Identification of Survival-Associated Splicing Factors in Lung Squamous Cell Carcinoma

et al. 2022

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Lung squamous cell carcinoma (LUSC) is a disease with high morbidity and mortality. Many studies have shown that aberrant alternative splicing (AS) can lead to tumorigenesis, and splicing factors (SFs) serve as an important function during AS. In this research, we propose an analysis method based on synergy to screen key factors that regulate the initiation and progression of LUSC. We first screened alternative splicing events (ASEs) associated with survival in LUSC patients by bivariate Cox regression analysis. Then an association network consisting of OS-ASEs, SFs, and their targeting relationship was constructed to identify key SFs. Finally, 10 key SFs were selected in terms of degree centrality. The validation on TCGA and cross-platform GEO datasets showed that some SFs were significantly differentially expressed in cancer and paracancer tissues, and some of them were associated with prognosis, indicating that our method is valid and accurate. It is expected that our method would be applied to a wide range of research fields and provide new insights in the future.

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Section: Methodsmentioning

confidence: 99%

Screening and Identification of Survival-Associated Splicing Factors in Lung Squamous Cell Carcinoma

et al. 2022

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“…Any genes with at least one database were counted as target genes of DEmiRNAs. Then, the intersection of DEmiRNAs predicted target genes and DEmRNAs were identified by the online Venn diagram tool (Evenn, http://www.ehbio.com/test/venn/#/ ) 24 and the overlapped genes were used to construct the miRNA–mRNA regulatory network using the Cytoscape software (Version 3.7.2, https://cytoscape.org/ ). 25 …”

Section: Methodsmentioning

confidence: 99%

Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

Liu¹,

He²,

Chen³

et al. 2022

IJGM

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Background Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circRNAs play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed to elucidate the underlying molecular mechanisms of circRNAs regulation in AD based on the circRNA-associated competing endogenous RNA (ceRNA) network. Methods Expression profiles of circRNAs (GSE97745), miRNAs (GSE92427), and mRNAs (GSE52093) were downloaded from Gene Expression Omnibus (GEO) databases, and the differentially expressed RNAs (DERNAs) were subsequently identified by bioinformatics analysis. CircRNA–miRNA–mRNA ceRNA network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to predict the potential functions of circRNA-associated ceRNA network. RNA was isolated from human arterial blood samples after which qRT-PCR was performed to confirm the DERNAs. Results We identified 14 (5 up-regulated and 9 down-regulated) differentially expressed circRNAs (DEcircRNAs), 17 (8 up-regulated and 9 down-regulated) differentially expressed miRNAs (DEmiRNAs) and 527 (297 up-regulated and 230 down-regulated) differentially expressed mRNAs (DEmRNAs) (adjusted P -value <0.05 and | log2FC | > 1.0). KEGG pathway analysis indicated that DEmRNAs were related to focal adhesion and extracellular matrix receptor interaction signaling pathways. Simultaneously, the present study constructed a ceRNA network based on 1 circRNAs (hsa_circRNA_082317), 1 miRNAs (hsa-miR-149-3p) and 10 mRNAs (MLEC, ENTPD7, SLC16A3, SLC7A8, TBC1D16, PAQR4, MAPK13, PIK3R2, ITGA5, SERPINA1). qRT-PCR demonstrated that hsa_circRNA_082317 and ITGA5 were significantly up-regulated, and hsa-miR-149-3p was dramatically down-regulated in AD (n = 3). Conclusion This is the first study to demonstrate the circRNA-associated ceRNA network is altered in AD, implying that circRNAs may play important roles in regulating the onset and progression and thus may serve as potential biomarkers for the diagnosis and treatment of AD.

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“…The data process for Cladograms were follows the guide of EasyAmplicon 1.14 [48], and finally visualized by ImageGP webserver 1.0 [49] by calling GraPhlAn v.0.9.7 [50]. The comparison known and novel taxonomy of copA genes is analyzed in Evenn webserver [51]…”

Section: Methodsmentioning

confidence: 99%

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes

Wang

et al. 2022

Preprint

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Exploring natural diversity of functional genes/proteins from environmental DNA (eDNA) in a high-throughput fashion remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 88 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high-confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually 175 novel copA sequences of high-quality were discovered. Phylogenetic analysis showed that almost all of these putative CopA proteins are distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (∆copA). Growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.

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EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online

Cited by 247 publications

References 17 publications

Screening and Identification of Survival-Associated Splicing Factors in Lung Squamous Cell Carcinoma

Screening and Identification of Survival-Associated Splicing Factors in Lung Squamous Cell Carcinoma

Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes

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