Grouping miRNAs of similar functions via weighted information content of gene ontology

Lan, Chaowang; Chen, Yi‐Ping Phoebe; Li, Jinyan

doi:10.1186/s12859-016-1367-0

Cited by 13 publications

(5 citation statements)

References 37 publications

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“…We hypothesized that when S. intermedius is damaged by environmental stresses, the expression of genes related to apoptosis and immunity is significant. Our results support the view that miRNA-target gene interactions are complex, and a single miRNA can regulate multiple target genes simultaneously, and a gene can be regulated by multiple miRNAs simultaneously (Agarwal et al 2015;Lan et al, 2016;Lai et al, 2022;Miao et al, 2022). The mechanism of the S. intermedius response to environmental stress is also complex.…”

Section: Effects Of the Combined Stresses On Mirna Regulation In S In...supporting

confidence: 84%

Sea Urchins in Acute High Temperature and Low Oxygen Environments: The Regulatory Role of microRNAs in Response to Environmental Stress

Han

Hao

et al. 2022

Front. Mar. Sci.

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Strongylocentrotus intermedius is an economically valuable sea urchin species in China. However, its growth and survival are severely constrained by ocean warming and the hypoxia that often accompanies high water temperatures. MicroRNAs (miRNAs) are important regulators of gene expression in response to environmental change. In this study, high-throughput RNA sequencing was used to investigate changes in miRNA expression in S. intermedius under heat (25°C), hypoxia (2 mg/L O2), and combined heat and hypoxia stresses. Twelve small RNAs libraries were constructed and 17, 14, and 23 differentially expressed miRNAs (DEMs) were identified in the heat, hypoxia, and combined stress groups (P<0.05), respectively. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional analyses of putative target genes of the DEMs suggested that these miRNAs were important in basal metabolism, apoptosis, oxidative stress, and immune-related pathways. By co-analysis with published transcriptome data, key DEMs (miR-193, miR-184, miR-133, miR-125, miR-2008) and their key target genes (EGF3, ABCB4, CYCL, PAN2, CALN) were identified. Quantitative real-time PCR analysis of the expression of 10 DEMs and their key target genes confirmed the RNA sequencing results. These results provide information on gene expression regulation of the molecular mechanisms underlying the response of S. intermedius to multi-cause environmental stresses.

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Section: Effects Of the Combined Stresses On Mirna Regulation In S In...supporting

confidence: 84%

Sea Urchins in Acute High Temperature and Low Oxygen Environments: The Regulatory Role of microRNAs in Response to Environmental Stress

Han

Hao

et al. 2022

Front. Mar. Sci.

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“…These genes play an important role in the UPR response to endoplasmic reticulum stress ( Gotoh et al, 2004 ; Sha et al, 2012 ). Our findings support the idea that miRNA-target gene interactions are complicated, and that a single miRNA can regulate multiple target genes simultaneously, whereas a single gene can be regulated by multiple miRNAs at the same time ( Lan et al, 2016 ). The results of the qRT-PCR validation further imply that there may be meaningful targeted regulatory interactions between th candidate DE miRNAs and DEGs.…”

Section: Discussionsupporting

confidence: 85%

Expression Regulation Mechanisms of Sea Urchin (Strongylocentrotus intermedius) Under the High Temperature: New Evidence for the miRNA-mRNA Interaction Involvement

Han

Quan

et al. 2022

Front. Genet.

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In the context of global warming and continuous high temperatures in the northern part of China during summer, the mortality rate of our main breeding species, Strongylocentrotus intermedius, reached 80% in 2020. How sea urchins respond to high temperatures is of great concern to academia and industry. In this study, we examined the antioxidant enzyme activities of different color tube-footed sea urchins under heat stress and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. The results showed that the antioxidant enzyme activities of sea urchins were altered by thermal stress, and the changes in peroxidase activities of red tube-footed sea urchins were particularly significant. Investigations revealed that 1,079 differentially expressed genes (DEGs), 11 DE miRNAs, and 104 “DE miRNA-DEG” pairs in total were detected in sea urchins under high temperature stress. Several mRNA and miRNAs were significantly changed (e.g. HSP70, DnaJ11, HYAL, CALR, miR-184-p5, miR-92a, miR-92c, and miR-124-p5), suggesting these genes and miRNAs exerted important functions in response to high temperature. At the transcriptional level, red tube-footed sea urchins were found to be more sensitive to high temperature and could respond to high temperature rapidly. DE miRNA-mRNA network showed that miR-92b-3p and PC-5p-7420 were the most corresponding miRNAs. Five mRNAs (DnaJ11, SAR1B, CALR, HYOU1, TUBA) may be potential markers of sea urchin response to high temperature. Possible interaction between miRNA-mRNA could be linked to protein folding in the endoplasmic reticulum, Phagosomes, and calcium transport. This study provides a theoretical basis for the molecular mechanism of sea urchin heat tolerance and information that will aid in the selection and breeding of sea urchins with high temperature tolerance.

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“…where ∩ and ∪ are "intersection" and "union" operators respectively. The GO terms of target proteins were downloaded from the EMBL-EBI website [26,27]. Drugs are expected to interact with proteins which have similar cellular components, or share similar molecular functions, or go through similar biological processes.…”

Section: Drug Target Protein Similaritymentioning

confidence: 99%

Inverse similarity and reliable negative samples for drug side-effect prediction

et al. 2019

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Background: In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computational methods mainly focus on leveraging validated drug side-effect relations for the prediction. The performance is severely impeded by the lack of reliable negative training data. Thus, a method to select reliable negative samples becomes vital in the performance improvement. Methods: Most of the existing computational prediction methods are essentially based on the assumption that similar drugs are inclined to share the same side-effects, which has given rise to remarkable performance. It is also rational to assume an inverse proposition that dissimilar drugs are less likely to share the same side-effects. Based on this inverse similarity hypothesis, we proposed a novel method to select highly-reliable negative samples for side-effect prediction. The first step of our method is to build a drug similarity integration framework to measure the similarity between drugs from different perspectives. This step integrates drug chemical structures, drug target proteins, drug substituents, and drug therapeutic information as features into a unified framework. Then, a similarity score between each candidate negative drug and validated positive drugs is calculated using the similarity integration framework. Those candidate negative drugs with lower similarity scores are preferentially selected as negative samples. Finally, both the validated positive drugs and the selected highly-reliable negative samples are used for predictions. Results: The performance of the proposed method was evaluated on simulative side-effect prediction of 917 DrugBank drugs, comparing with four machine-learning algorithms. Extensive experiments show that the drug similarity integration framework has superior capability in capturing drug features, achieving much better performance than those based on a single type of drug property. Besides, the four machine-learning algorithms achieved significant improvement in macro-averaging F1-score (e.g., SVM from 0.655 to 0.898), macro-averaging precision (e.g., RBF from 0.592 to 0.828) and macro-averaging recall (e.g., KNN from 0.651 to 0.772) complimentarily attributed to the highly-reliable negative samples selected by the proposed method. Conclusions:The results suggest that the inverse similarity hypothesis and the integration of different drug properties are valuable for side-effect prediction. The selection of highly-reliable negative samples can also make significant contributions to the performance improvement.

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Grouping miRNAs of similar functions via weighted information content of gene ontology

Cited by 13 publications

References 37 publications

Sea Urchins in Acute High Temperature and Low Oxygen Environments: The Regulatory Role of microRNAs in Response to Environmental Stress

Sea Urchins in Acute High Temperature and Low Oxygen Environments: The Regulatory Role of microRNAs in Response to Environmental Stress

Expression Regulation Mechanisms of Sea Urchin (Strongylocentrotus intermedius) Under the High Temperature: New Evidence for the miRNA-mRNA Interaction Involvement

Inverse similarity and reliable negative samples for drug side-effect prediction

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