scholarly journals RFMirTarget: A Random Forest Classifier for Human miRNA Target Gene Prediction

2012 ◽  
pp. 97-108 ◽  
Author(s):  
Mariana R. Mendoza ◽  
Guilherme C. da Fonseca ◽  
Guilherme L. de Morais ◽  
Ronnie Alves ◽  
Ana L. C. Bazzan ◽  
...  
Keyword(s):  
Random Forest ◽  
Mirna Target ◽  
Target Gene ◽  
Gene Prediction ◽  
Random Forest Classifier ◽  
Mirna Target Gene

Study on the Function of miRNA-155 Target Using Bioinformatics Methods

2013 ◽  
Vol 709 ◽  
pp. 858-861
Author(s):  
De Ming Han ◽  
Zi Jun Shen ◽  
Li Hui Zhao
Keyword(s):  
Protein Expression ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Diagnosis And Treatment ◽  
Transcriptional Level ◽  
Mirna Target Gene ◽  
Non Coding Rnas

MicroRNAs are small non-coding RNAs that act at the post-transcriptional level, regulating protein expression by repressing translation or destabilizing mRNA target. We searched information about miR-155 in miRBase. Target genes of miR-155 are predicted by four miRNA target gene prediction softwares. The result shows that miR-155 was involved in proliferation, differentiation and apoptosis. These results can contribute to further study on the role of microRNA in diagnosis and treatment of cancer.

scholarly journals miR-184 Inhibits Tumor Invasion, Migration and Metastasis in Nasopharyngeal Carcinoma by Targeting Notch2

2018 ◽  
Vol 49 (4) ◽  
pp. 1564-1576 ◽  
Author(s):  
Hong-Ming Zhu ◽  
Xue-Song Jiang ◽  
Hui-Zi Li ◽  
Lu-Xi Qian ◽  
Ming-Yu Du ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Cell Invasion ◽  
Mirna Target ◽  
Target Gene ◽  
Gene Prediction ◽  
Luciferase Reporter Assay ◽  
Luciferase Reporter ◽  
Reporter Assay ◽  
Mirna Target Gene ◽  
Dual Luciferase Reporter Assay

Background/Aims: A recent study found that dysregulated microRNA-184 (miR-184) is involved in the proliferation and survival of nasopharyngeal carcinoma (NPC). This study aimed to evaluate the detailed mechanisms of invasion, migration and metastasis of NPC cells. Methods: Quantitative reverse-transcription PCR (qRT-PCR) and Western blot were used to confirm the expression levels of miR-184 and Notch2. NPC cell invasion and migration were subsequently examined using in vitro cell invasion and wound-healing assays, respectively. MicroRNA (miRNA) target gene prediction databases and dual-luciferase reporter assay were adopted to validate the target genes of miR-184. Results: MiR-184 was downregulated in the NPC cell lines. The miR-184 inhibitor increased the number of invading NPC cells, whereas miR-184 mimics inhibited the invasive ability of such cells. The protein level of E-cadherin decreased, whereas those of N-cadherin and vimentin increased in the anti-miR-184 group. This result showed that miR-184 inhibited NPC cell invasion and metastasis by regulating EMT progression. MiRNA target gene prediction databases indicated the potential of Notch2 as a direct target gene of miR-184. Such a notion was then validated by results of dual-luciferase reporter assay. Notably, shRNANotch2 restrained the EMT and partially abrogated the inhibitory effects of miR-184 on EMT progression in NPC cells. Conclusion: MiR-184 functions as a tumour-suppressive miRNA targeting Notch2 and inhibits the invasion, migration and metastasis of NPC.

scholarly journals Identification of genes, pathways and transcription factor-miRNA-target gene networks and experimental verification in venous thromboembolism

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yiming Su ◽  
Qiyi Li ◽  
Zhiyong Zheng ◽  
Xiaomin Wei ◽  
Peiyong Hou
Keyword(s):  
Transcription Factor ◽  
Venous Thromboembolism ◽  
Cellular Response ◽  
Gene Network ◽  
Mirna Target ◽  
Target Gene ◽  
Vascular Endothelial Cell ◽  
Differentially Expressed ◽  
Ppi Network ◽  
Mirna Target Gene

AbstractVenous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction. However, the exact pathogenesis and underlying mechanisms of VTE are not completely clear. The aim of this study was to identify the core genes and pathways in VECs that are involved in the development and progression of unprovoked VTE (uVTE). The microarray dataset GSE118259 was downloaded from the Gene Expression Omnibus database, and 341 up-regulated and 8 down-regulated genes were identified in the VTE patients relative to the healthy controls, including CREB1, HIF1α, CBL, ILK, ESM1 and the ribosomal protein family genes. The protein–protein interaction (PPI) network and the transcription factor (TF)-miRNA-target gene network were constructed with these differentially expressed genes (DEGs), and visualized using Cytoscape software 3.6.1. Eighty-nine miRNAs were predicted as the targeting miRNAs of the DEGs, and 197 TFs were predicted as regulators of these miRNAs. In addition, 237 node genes and 4 modules were identified in the PPI network. The significantly enriched pathways included metabolic, cell adhesion, cell proliferation and cellular response to growth factor stimulus pathways. CREB1 was a differentially expressed TF in the TF-miRNA-target gene network, which regulated six miRNA-target gene pairs. The up-regulation of ESM1, HIF1α and CREB1 was confirmed at the mRNA and protein level in the plasma of uVTE patients. Taken together, ESM1, HIF1α and the CREB1-miRNA-target genes axis play potential mechanistic roles in uVTE development.

scholarly journals Profiling the Abiotic Stress Responsive microRNA Landscape of Arabidopsis thaliana

Plants ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 58 ◽  
Author(s):  
Joseph Pegler ◽  
Jackson Oultram ◽  
Christopher Grof ◽  
Andrew Eamens
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Mirna Target ◽  
Target Gene ◽  
Negative Impact ◽  
Mirna Target Gene ◽  
Target Gene Expression ◽  
Response Phenotype

It is well established among interdisciplinary researchers that there is an urgent need to address the negative impacts that accompany climate change. One such negative impact is the increased prevalence of unfavorable environmental conditions that significantly contribute to reduced agricultural yield. Plant microRNAs (miRNAs) are key gene expression regulators that control development, defense against invading pathogens and adaptation to abiotic stress. Arabidopsis thaliana (Arabidopsis) can be readily molecularly manipulated, therefore offering an excellent experimental system to alter the profile of abiotic stress responsive miRNA/target gene expression modules to determine whether such modification enables Arabidopsis to express an altered abiotic stress response phenotype. Towards this goal, high throughput sequencing was used to profile the miRNA landscape of Arabidopsis whole seedlings exposed to heat, drought and salt stress, and identified 121, 123 and 118 miRNAs with a greater than 2-fold altered abundance, respectively. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) was next employed to experimentally validate miRNA abundance fold changes, and to document reciprocal expression trends for the target genes of miRNAs determined abiotic stress responsive. RT-qPCR also demonstrated that each miRNA/target gene expression module determined to be abiotic stress responsive in Arabidopsis whole seedlings was reflective of altered miRNA/target gene abundance in Arabidopsis root and shoot tissues post salt stress exposure. Taken together, the data presented here offers an excellent starting platform to identify the miRNA/target gene expression modules for future molecular manipulation to generate plant lines that display an altered response phenotype to abiotic stress.

scholarly journals The integrative knowledge base for miRNA-mRNA expression in colorectal cancer

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Daša Jevšinek Skok ◽  
Nina Hauptman ◽  
Emanuela Boštjančič ◽  
Nina Zidar
Keyword(s):  
Colorectal Cancer ◽  
Knowledge Base ◽  
Mrna Expression ◽  
Web Application ◽  
Mirna Target ◽  
Target Gene ◽  
The Cancer Genome Atlas ◽  
Gene Expressions ◽  
Mirna Target Gene ◽  
Colon And Rectum

Abstract“miRNA colorectal cancer” (https://mirna-coadread.omics.si/) is a freely available web application for studying microRNA and mRNA expression and their correlation in colorectal cancer. To the best of our knowledge, “miRNA colorectal cancer” has the largest knowledge base of miRNA-target gene expressions and correlations in colorectal cancer, based on the largest available sample size from the same source of data. Data from high-throughput molecular profiling of 295 colon and rectum adenocarcinoma samples from The Cancer Genome Atlas was analyzed and integrated into our knowledge base. The objective of developing this web application was to help researchers to discover the behavior and role of miRNA-target gene interactions in colorectal cancer. For this purpose, results of differential expression and correlation analyses of miRNA and mRNA data collected in our knowledge base are available through web forms. To validate our knowledge base experimentally, we selected genes FN1, TGFB2, RND3, ZEB1 and ZEB2 and miRNAs hsa-miR-200a/b/c-3p, hsa-miR-141-3p and hsa-miR-429. Both approaches revealed a negative correlation between miRNA hsa-miR-200b/c-3p and its target gene FN1 and between hsa-miR-200a-3p and its target TGFB2, thus supporting the usefulness of the developed knowledge base.

scholarly journals Association of Extracellular Signal-Regulated Kinase Genes With Myopia: A Longitudinal Study of Chinese Children

2021 ◽  
Vol 12 ◽  
Author(s):  
Haishao Xiao ◽  
Shudan Lin ◽  
Dandan Jiang ◽  
Yaoyao Lin ◽  
Linjie Liu ◽  
...  
Keyword(s):  
Longitudinal Study ◽  
Gene Network ◽  
Mirna Target ◽  
Target Gene ◽  
Target Genes ◽  
Chinese Children ◽  
Indirect Interaction ◽  
Mirna Target Gene ◽  
Extracellular Signal Regulated Kinase ◽  
Extracellular Signal

Graphical AbstractThe genes in the miRNA-target gene network represent the intersection of the target genes and the genes from String that had direct or indirect interaction relationships with significant genes.

scholarly journals Genome-Wide Analysis of Coding and Non-coding RNA Reveals a Conserved miR164–NAC–mRNA Regulatory Pathway for Disease Defense in Populus

2021 ◽  
Vol 12 ◽  
Author(s):  
Sisi Chen ◽  
Jiadong Wu ◽  
Yanfeng Zhang ◽  
Yiyang Zhao ◽  
Weijie Xu ◽  
...  
Keyword(s):  
Plant Defense ◽  
Messenger Rna ◽  
Mirna Target ◽  
Target Gene ◽  
Black Spot ◽  
Defense Responses ◽  
Plant Colonization ◽  
Post Inoculation ◽  
Mirna Target Gene ◽  
Gene Pairs

MicroRNAs (miRNAs) contribute to plant defense responses by increasing the overall genetic diversity; however, their origins and functional importance in plant defense remain unclear. Here, we employed Illumina sequencing technology to assess how miRNA and messenger RNA (mRNA) populations vary in the Chinese white poplar (Populus tomentosa) during a leaf black spot fungus (Marssonina brunnea) infection. We sampled RNAs from infective leaves at conidia germinated stage [12 h post-inoculation (hpi)], infective vesicles stage (24 hpi), and intercellular infective hyphae stage (48 hpi), three essential stages associated with plant colonization and biotrophic growth in M. brunnea fungi. In total, 8,938 conserved miRNA-target gene pairs and 3,901 Populus-specific miRNA-target gene pairs were detected. The result showed that Populus-specific miRNAs (66%) were more involved in the regulation of the disease resistance genes. By contrast, conserved miRNAs (>80%) target more whole-genome duplication (WGD)-derived transcription factors (TFs). Among the 1,023 WGD-derived TF pairs, 44.9% TF pairs had only one paralog being targeted by a miRNA that could be due to either gain or loss of a miRNA binding site after the WGD. A conserved hierarchical regulatory network combining promoter analyses and hierarchical clustering approach uncovered a miR164–NAM, ATAF, and CUC (NAC) transcription factor–mRNA regulatory module that has potential in Marssonina defense responses. Furthermore, analyses of the locations of miRNA precursor sequences reveal that pseudogenes and transposon contributed a certain proportion (∼30%) of the miRNA origin. Together, these observations provide evolutionary insights into the origin and potential roles of miRNAs in plant defense and functional innovation.

scholarly journals Development of Incompletely Fused Carpels in Maize Ovary Revealed by miRNA, Target Gene and Phytohormone Analysis

2017 ◽  
Vol 8 ◽  
Author(s):  
Hongping Li ◽  
Ting Peng ◽  
Qun Wang ◽  
Yufeng Wu ◽  
Jianfeng Chang ◽  
...  
Keyword(s):  
Mirna Target ◽  
Target Gene ◽  
Mirna Target Gene

scholarly journals MicroRNA-Mediated Responses to Cadmium Stress in Arabidopsis thaliana

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 130
Author(s):  
Joseph L. Pegler ◽  
Jackson M. J. Oultram ◽  
Duc Quan Nguyen ◽  
Christopher P. L. Grof ◽  
Andrew L. Eamens
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Mirna Target ◽  
Target Gene ◽  
Rna Binding ◽  
Molecular Response ◽  
Cd Stress ◽  
Mirna Target Gene ◽  
Target Gene Expression ◽  
Essential Heavy Metal

In recent decades, the presence of cadmium (Cd) in the environment has increased significantly due to anthropogenic activities. Cd is taken up from the soil by plant roots for its subsequent translocation to shoots. However, Cd is a non-essential heavy metal and is therefore toxic to plants when it over-accumulates. MicroRNA (miRNA)-directed gene expression regulation is central to the response of a plant to Cd stress. Here, we document the miRNA-directed response of wild-type Arabidopsis thaliana (Arabidopsis) plants and the drb1, drb2 and drb4 mutant lines to Cd stress. Phenotypic and physiological analyses revealed the drb1 mutant to display the highest degree of tolerance to the imposed stress while the drb2 mutant was the most sensitive. RT-qPCR-based molecular profiling of miRNA abundance and miRNA target gene expression revealed DRB1 to be the primary double-stranded RNA binding (DRB) protein required for the production of six of the seven Cd-responsive miRNAs analyzed. However, DRB2, and not DRB1, was determined to be required for miR396 production. RT-qPCR further inferred that transcript cleavage was the RNA silencing mechanism directed by each assessed miRNA to control miRNA target gene expression. Taken together, the results presented here reveal the complexity of the miRNA-directed molecular response of Arabidopsis to Cd stress.

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