GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins

Xia, Mengxuan; Liu, Chunjie; Zhang, Qiong; Guo, An‐Yuan

doi:10.3390/cells8070675

Cited by 25 publications

(22 citation statements)

References 12 publications

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“…CDC25B was reported to be the direct target of miR-214 [21]. CDC25B was dramatically elevated in multiple cancer, which was validated by the pan-cancer analysis from GEDS [22] and Uclcan [23] (Fig. 7A,7C).…”

Section: The Role Of Cdc25b In Escc and The Association Between Cdc25mentioning

confidence: 57%

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B Axis

Jia

Chu

et al. 2020

Preprint

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Background Recently, extensive researches have established that long non-coding RNA (lncRNA) was an important factor that is strongly related to carcinogenesis. However, the function of lncRNAs in esophageal cell squamous carcinoma (ESCC) remains to be explored. In the current study, we assessed the expression pattern and the biological function of FAM83A-AS1 in ESCC. Methods qRT-PCR was used to detect the expression of FAM83A-AS1,miR-214, and CDC25B expression in ESCCtissues and cell lines. Cell counting kit 8 (CCK-8, Transwell, apoptosis, and cell cycle assays were performed to define the function of FAM83A-AS1 in ESCC cell. Furthermore, the regulation of miR-214 by FAM83A-AS1 was defined by qRT- PCR and rescue assays.In addition, the association between CDC25B,miR-214,CDC25B were performed with qRT-PCR.Results: Here we discovered that FAM83A-AS1 was strongly expressed in ESCC tissues. FAM83A-AS1 abundance was associated with TNM stages and the differentiation grade of ESCC patients. The receiver operating characteristic curve (ROC) analysis indicated the high accuracy of FAM83A-AS1 in ESCC diagnosis. Functionally, inhibiting FAM83A-AS1 repressed cell proliferation, migration, and invasion in ESCC. In addition, we found that FAM83A-AS1 accelerated cell cycle and inhibited cell apoptosis. Mechanistically, we found that FAM83A-AS1 regulated miR-214 expression and there was a negative correlation between miR-214 and FAM83A-AS1 in ESCC. Rescue assay indicated that miR-214 could impair the suppressing effect of cell migration induced by FAM83A-AS1 depletion. Furthermore, CDC25B was a direct target of miR-214 and FAM83A-AS1 enhanced CDC25B expression while miR-214 positively CDC25B expression in ESCC. Conclusions Collectively, we concluded that FAM83A-AS1 facilitated ESCC progression by regulating the miR-214/CDC25B axis. Our study showed FAM83A-AS1 may act as a target for ESCC diagnosis and therapy.

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Section: The Role Of Cdc25b In Escc and The Association Between Cdc25mentioning

confidence: 57%

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B Axis

Jia

Chu

et al. 2020

Preprint

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“…Gene Expression Display Server (GEDS, http://bioinfo. life.hust.edu.cn/web/GEDS/) was used to explore the expression pattern of miR-31-5p in COAD [42]. GEDS is a platform that collects 40 tissues and 1,594 cells lines from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), and MD Anderson Cell Lines Project (MCLP), providing information on human gene, miRNA, and protein expression in tissues and cell lines.…”

Section: Expression Level Of Mir-31-5p In Coadmentioning

confidence: 99%

High miR-31-5p expression promotes colon adenocarcinoma progression by targeting TNS1

et al. 2020

Aging

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Overexpression of the miR-31-5p contributes to tumorigenesis and metastasis in diverse neoplasms. In this study, we evaluated expression of miR-31-5p in patients with colon adenocarcinoma (COAD). We found that miR-31-5p was overexpressed in four cohorts (GSE30454, GSE41655, GSE18392, GSE108153) of COAD patients. Importantly, a LinkedOmics analysis revealed that high miR-31-5p expression was associated with poor overall survival of COAD patients. At total of 133 putative target genes of miR-31-5p were identified from TargetScan, miRDB, and TargetMiner. After integrating the target genes with 1,556 deregulated genes in COAD, 8 were acquired that may be targeted by miR-31-5p and contribute to COAD progression. Among these, tensin 1 (TNS1) showed the greatest prognostic ability in COAD and was strongly correlated with M2 macrophages, regulatory T cells, and other immune cells. These findings indicate that, in COAD, miR-31-5p is a potential prognostic factor that affects immune infiltration by targeting TNS1.

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“…The dysregulated miRNAs not only differentially expressed between the CRC cancer samples and normal samples, but also associated with the prognosis of CRC patients were identi ed as key miRNAs in human CRC and were chosen for subsequent research, according to the criteria of a Pvalue < 0.05. In addition, we further validated the expression pattern of key miRNAs in multiple types of cancer by using the Gene Expression Display Server (GEDS, http://bioinfo.life.hust.edu.cn/web/GEDS/) database, a web-based tool for quanti cation, comparison and visualization of gene expression data based on The Cancer Genome Atlas, Genotype-Tissue Expression (GETx), Cancer Cell Line Encyclopedia (CCLE), and MD Anderson Cell Lines Project (MCLP) databases [17].…”

Section: Identi Cation Of Key Mirnasmentioning

confidence: 99%

Identification of Novel Survival Related lncRNA-miRNA-mRNA Competing Endogenous RNA Network Associated with Immune Infiltration in Colorectal Cancer

Han

Wang

et al. 2020

Preprint

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Background: Increasing studies have reported that long noncoding RNAs (lncRNAs) play critical roles in the initiation and progression of carcinogenesis. However, the underlying regulatory mechanisms of lncRNA related competing endogenous RNA (ceRNA) network in colorectal cancer (CRC) are not fully understood.Methods: Dysregulated microRNAs (miRNAs) in CRC samples were screened from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. After that, the key miRNAs were filtered out through a comprehensive assessment of their expression levels and prognostic values. Subsequently, the targeted downstream mRNAs and upstream lncRNAs of the key miRNAs were predicted by using multiple bioinformatic databases. A ceRNA network was constructed by using Cytoscape, and the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on this network using the DAVID database. Ultimately, expression levels and prognostic values of the lncRNAs and mRNAs were evaluated, and a survival related ceRNA network was constructed and visualized by using Cytoscape. In addition, the Gene Set Enrichment Analysis (GSEA) software package was employed to identify the pathways in which this survival related ceRNA network was enriched. Furthermore, correlations of ceRNA network with immune infiltration level were estimated by the Tumor Immune Estimation Resource (TIMER) databases.Results: In total, 28 dysregulated miRNAs were obtained, and two of them were identified as key miRNAs based on expression levels and prognostic values analyses. Subsequently, a total of three upstream lncRNAs and 309 downstream mRNAs were predicted by using bioinformatic tools, and two key lncRNAs and eight key mRNAs were identified by expression and survival analysis. A ceRNA regulatory network associated with the prognosis of CRC patients was constructed. Furthermore, GSEA analysis indicated the possible association of key mRNAs with CRC onset and progression. Importantly, immune infiltration analysis revealed that the ceRNA network was remarkably associated with infiltration abundance of multiple immune cells and expression levels of immune checkpoints.Conclusions: We constructed a survival related ceRNA regulatory network in human CRC, NEAT1 and XIST are potential prognostic factors that affect CRC onset and progression by targeting miR-195-5p.

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GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins

Cited by 25 publications

References 12 publications

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B Axis

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B Axis

High miR-31-5p expression promotes colon adenocarcinoma progression by targeting TNS1

Identification of Novel Survival Related lncRNA-miRNA-mRNA Competing Endogenous RNA Network Associated with Immune Infiltration in Colorectal Cancer

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GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins

Cited by 25 publications

References 12 publications

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B&nbsp;Axis

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B&nbsp;Axis

High miR-31-5p expression promotes colon adenocarcinoma progression by targeting TNS1

Identification of Novel Survival Related lncRNA-miRNA-mRNA Competing Endogenous RNA Network Associated with Immune Infiltration in Colorectal Cancer

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LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B Axis

LncRNA FAM83A-AS1 Dives ESCC Progression by Regulating miR-214/CDC25B Axis