Identification of associations between small molecule drugs and miRNAs based on functional similarity

Wang, Jing; Meng, Fengyan; Dai, Erfu; Yang, Feng; Wang, Shuyuan; Chen, Xiaowen; Yang, Lei; Wang, Yuwen; Jiang, Wei

doi:10.18632/oncotarget.9577

Cited by 32 publications

(23 citation statements)

References 65 publications

(66 reference statements)

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“…The present study used TCGA data and three GEO datasets to identify common dysregulated miRNAs in GC. A similar analysis has also been reported by a number of other groups (16)(17)(18)(19).…”

Section: Methodssupporting

confidence: 86%

Integrated miRNA profiling and bioinformatics analyses reveal upregulated miRNAs in gastric cancer

Yuan

Zhang

et al. 2019

Oncol Lett

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Gastric cancer is one of the most common malignancies in China and exhibits a poor prognosis. The most significant challenge for gastric cancer treatment is the absence of early diagnostic biomarkers. MicroRNAs (miRNAs) are small non-coding RNAs, which possess clinical value in a number of different types of cancer. The current study identified 13 miRNAs (hsa-miR-22, hsa-miR-545, hsa-let-7i, hsa-miR-15b, hsa-miR-221, hsa-miR-196a, hsa-miR-20a, hsa-miR-196b, hsa-miR-93, hsa-miR-19a, hsa-miR-503, hsa-miR-106b and hsa-miR-18a) that were significantly overexpressed in GC, by analyzing 1,000 GC samples included in four public datasets, including GSE23739, GSE78091, GSE30070 and The Cancer Genome Atlas. Furthermore, it was revealed that the expression levels of these 13 miRNAs were significantly higher in gastric cancer tissues of grades I, II and III compared with normal controls. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that the differentially expressed miRNAs were involved in regulating transcription, protein amino acid phosphorylation, signal transduction, protein binding, zinc ion binding, the mitogen-activated protein kinase signaling pathway and focal adhesion. In summary, the present study may provide potential new therapeutic and prognostic targets for gastric cancer.

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Section: Methodssupporting

confidence: 86%

Integrated miRNA profiling and bioinformatics analyses reveal upregulated miRNAs in gastric cancer

Yuan

Zhang

et al. 2019

Oncol Lett

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“…Another common approach is to identify drug-miRNA relationships by comparing disease molecular features and drug molecular features, such as gene expression. Wang et al [65] proposed a novel computational approach to identify associations between small molecules and miRNAs based on functional similarity of DEG. The results show 2265 associations between FDA-approved drugs and diseases, where 35% of the associations have been reported in the literature.…”

Section: Discovering Novel Phenotypic Relationsmentioning

confidence: 99%

“…Also, 19 potential drugs were identified for breast cancer, in which 12 drugs were reported by previous studies. Their studies provide a valuable perspective for repurposing drugs and predicting novel drug targets, which may provide new way for miRNA-targeted therapy [65].…”

Section: Discovering Novel Phenotypic Relationsmentioning

confidence: 99%

A review of connectivity map and computational approaches in pharmacogenomics

et al. 2017

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Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.

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“…First, we downloaded the gene expression profiles under small molecule perturbations in Cmap [ 47 ]. Then, DE genes were obtained for each instance according to the previous study [ 48 ]. Eight drugs could reverse at least three genes’ expression ( Supplementary Table S5 ), but the associations with bone loss had not been reported.…”

Section: Resultsmentioning

confidence: 99%

Integrative Analysis of Regulatory Module Reveals Associations of Microgravity with Dysfunctions of Multi-body Systems and Tumorigenesis

Yuan

Liu

Zhou

et al. 2020

IJMS

Self Cite

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Previous studies have demonstrated that microgravity could lead to health risks. The investigation of the molecular mechanisms from the aspect of systems biology has not been performed yet. Here, we integratively analyzed transcriptional and post-transcriptional regulations based on gene and miRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity. Two hundred and thirty dysregulated TF-miRNA (transcription factor and microRNA) feed-forward loops (FFLs) were identified in microgravity. The immune, cardiovascular, endocrine, nervous and skeletal system subnetworks were constructed according to the functions of dysregulated FFLs. Taking the skeletal system as an example, most of genes and miRNAs in the subnetwork were involved in bone loss. In addition, several drugs have been predicted to have potential to reduce bone loss, such as traditional Chinese medicines Emodin and Ginsenoside Rh2. Furthermore, we investigated the relationships between microgravity and 20 cancer types, and found that most of cancers might be promoted by microgravity. For example, rectum adenocarcinoma (READ) might be induced by microgravity through reducing antigen presentation and suppressing IgA-antibody-secreting cells’ migration. Collectively, TF-miRNA FFL might provide a novel mechanism to elucidate the changes induced by microgravity, serve as drug targets to relieve microgravity effects, and give new insights to explore the relationships between microgravity and cancers.

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Identification of associations between small molecule drugs and miRNAs based on functional similarity

Cited by 32 publications

References 65 publications

Integrated miRNA profiling and bioinformatics analyses reveal upregulated miRNAs in gastric cancer

Integrated miRNA profiling and bioinformatics analyses reveal upregulated miRNAs in gastric cancer

A review of connectivity map and computational approaches in pharmacogenomics

Integrative Analysis of Regulatory Module Reveals Associations of Microgravity with Dysfunctions of Multi-body Systems and Tumorigenesis

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