Identification of Key Genes Affecting Results of Hyperthermia in Osteosarcoma Based on Integrative ChIP-Seq/TargetScan Analysis

Shi, Yong; Yang, Fan; Wei, Shuqing; Xu, Gang

doi:10.12659/msm.901191

Cited by 41 publications

(27 citation statements)

References 47 publications

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“…Shortlisted circRNA-interacting miRNAs were further analyzed by mirPath v.3 (Vlachos et al, 2015) and TargetScan (Shi et al, 2017), leading to the discovery of pathways that may be mediated by circRNA-miRNA interactions. Pathway/category union was predicted by mirPath v.3 (Vlachos et al, 2015) and TargetScan (Shi et al, 2017), which identified all the pathways significantly targeted by the selected microRNAs. Fisher's meta-analysis method was used to calculate the significance levels and extract the merged p-values for each pathway.…”

Section: Pathway Analysis Of the Circrna-mirna Targeted Genesmentioning

confidence: 99%

Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

Mai

et al. 2020

Front. Neurosci.

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Many hospitals lack facilities for accurate diagnosis of acute ischemic stroke (AIS). Circular RNA (circRNA) is highly expressed in the brain and is closely associated with stroke. In this study, we examined whether the blood-borne circRNAs could be promising candidates as adjunctive diagnostic biomarkers and their pathophysiological roles after stroke. We profiled the blood circRNA expression in mice subjected to experimental focal cerebral ischemia and validated the selected circRNAs in AIS patients. We demonstrated that 128, 198, and 789 circRNAs were significantly altered at 5 min, 3 h, and 24 h after ischemic stroke, respectively. Our bioinformatics analysis revealed that the circRNA-targeted genes were associated with the Hippo signaling pathway, extracellular matrix-receptor interaction, and fatty acid metabolism at 5 min, 3 h and 24 h after ischemic stroke, respectively. We verified that many of these circRNAs existed in the mouse brain. Furthermore, we found that most of the predicted circRNA-miRNA interactions apparently exhibited functional roles in terms of regulation of their target gene expression in the brain. We also verified that many of these mouse circRNAs were conserved in human. Finally, we found that circBBS2 and circPHKA2 were differentially expressed in the blood of AIS patients. These results demonstrate that blood circRNAs may serve as potential biomarkers for AIS diagnosis and reveal the pathophysiological responses in the brain after ischemic stroke.

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Section: Pathway Analysis Of the Circrna-mirna Targeted Genesmentioning

confidence: 99%

Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

Mai

et al. 2020

Front. Neurosci.

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“…miRanda was used to match the entire miRNA sequences. The TargetScan (Shi et al, 2017) parameters were set as a context score percentile >50. The miRanda parameters (John et al, 2004) were set as free energy <−10 kcal/mol and a score >50.…”

Section: Bioinformatics Analysis Of Mrna and Mirna Transcriptome Datamentioning

confidence: 99%

Gonad-Specific Transcriptomes Reveal Differential Expression of Gene and miRNA Between Male and Female of the Discus Fish (Symphysodon aequifasciatus)

Wen

et al. 2020

Front. Physiol.

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The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. In artificial reproduction, they must be matched by one male and one female, whereas phenotype investigation indicated that there are no significant differences in appearance between males and females, which causes great difficulties in the mating during artificial reproduction. So, it is of great importance to establish artificial sex identification methods for the discus fish. The molecular mechanism of the sexual dimorphism of the discus fish was previously unknown. In this study, we constructed six cDNA libraries from three adult testes and three adult ovaries and performed RNA sequencing for identifying sex-biased candidate genes and microRNAs (miRNAs). A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries. A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries. Eight differentially expressed unigenes, seven differentially expressed miRNAs and one non-differential miRNA were validated by quantitative real-time polymerase chain reaction. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 miRNA-mRNA interaction pairs, and some of vital sex-related metabolic pathways were also identified. These results revealed these differentially expressed genes and miRNAs between ovary and testis might be involved in regulating gonadal development, sex determination, gametogenesis, and physiological function maintenance, and there are complex regulatory networks between genes and miRNAs. It can help us understand the molecular mechanism of the sexual dimorphism and obtain a high-efficiency sex identification method in the artificial reproduction process of the discus fish.

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“…The target genes of miRNA-146a-5p were predicted by Targetscan [10] (http://www.targetscan.org/vert_72/), miRDB [11] (http://mirdb.org/), miRWalk [12] (http://zmf.umm.uniheidelberg.de/apps/zmf/mirwalk/), and PicTar [13] (https://pictar.mdc-berlin.de/), the results were admitted into draw Venn diagram [14] and the results belonged to the 4 databases were selected. Then we get the sequence of miRNA-146a-5p and the target gene and look for the combining site to identify the relationship between them.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

The expression of miRNA-146a-5p and its mechanism of treating dry eye syndrome

Yin

Zhang

et al. 2020

Preprint

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Background: Dry eye syndrome in which tear fluid quality or abnormality or kinetic abnormality is caused by many causes, resulting in decreased tear film stability. In recent years, more and more results from the studies indicate that miRNA alterations are involved in dry eye syndrome. And miRNA-146a-5p is a key regulator to regulate the inflammatory response. In this paper, we demonstrated whether miRNA-146a-5p could cure dry eye syndrome by regulating target genes based on network analysis.Methods: In this paper, we collected the blood of patients with dry eye disease which served as a model group, the blood of healthy people was used as a control group. The expression of miRNA-146a-5p in the patients was detected by RT-PCR, the genes controlled by miRNA-146a-5p were predicted by Targetscan, miRDB, miRWalk and PicTar databases, the genes regulated by miRNA-146a-5p which is related to dry eye disease were selected by draw Venn diagram;Results: The comparison of the general information between patients and healthy people was no significant difference, and it indicated that the two groups were comparable. The results of databases showed that IRAK1 was one of the target genes regulated by miRNA-146a-5p and it is related to dry eye disease. The expression of miRNA-146a-5p was negatively related to IRAK1 mRNA and protein. While IRAK1 had positive correlation with IL-6, TNF-α and CBP proteins. Conclusion: These results emphasized that miRNA-146a-5p could inhibit the expression of IRAK1, IL-6, TNF-α and CBP so as to help reduce the inflammatory response in dry eye syndrome.

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Identification of Key Genes Affecting Results of Hyperthermia in Osteosarcoma Based on Integrative ChIP-Seq/TargetScan Analysis

Cited by 41 publications

References 47 publications

Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

Gonad-Specific Transcriptomes Reveal Differential Expression of Gene and miRNA Between Male and Female of the Discus Fish (Symphysodon aequifasciatus)

The expression of miRNA-146a-5p and its mechanism of treating dry eye syndrome

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