Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses

Jiang, Wei; Chen, Xiaowen; Liao, Mingzhi; Li, Wei; Lian, Baofeng; Wang, Lihong; Meng, Fengyan; Liu, Xinyi; Chen, Xiujie; Jin, Yan; Li, Xia

doi:10.1038/srep00282

Cited by 68 publications

(60 citation statements)

References 54 publications

(70 reference statements)

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“…In addition, a similar approach of CMap application has been used to investigate relationships between drugs and microRNAs (miRNAs) [64]. Jiang et al proposed a novel high-throughput approach to identify the biological links between drugs and miRNAs in 23 different cancers and constructed the Small Molecule-MiRNA Network for each cancer to systematically analyze the properties of their associations.…”

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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Section: Discovering Novel Phenotypic Relationsmentioning

confidence: 99%

A review of connectivity map and computational approaches in pharmacogenomics

et al. 2017

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“…Due to large collections of transcriptional and drug data being available, new computational methods for identification of miRNAs as potential drug targets have recently been proposed. For example, Jiang et al [145] proposed a framework for construction of a network, SMirN, of interactions between small drug molecules (compounds) and miRNAs using data from different human cancers. Specifically, they used transcriptional responses to compounds and differentially expressed miRNA target genes in 23 different human cancers.…”

Section: Computational Methods For Drug Repurposing and Personalised mentioning

confidence: 99%

“…SmirN [145] Inference of drug-miRAN network by integrating cancer related miRNA target gene expression and transcriptional responses to drug compounds.…”

Section: Databasementioning

confidence: 99%

Integrative methods for analyzing big data in precision medicine

2016

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We provide an overview of recent developments in big data analyses in the context of precision medicine and health informatics. With the advance in technologies capturing molecular and medical data, we entered the area of Big Data in biology and medicine. These data offer many opportunities to advance precision medicine.We outline key challenges in precision medicine and present recent advances in data integrationbased methods to uncover personalized information from big data produced by various omics studies. We survey recent integrative methods for disease subtyping, bio-markers discovery and drug repurposing, and list the tools that are available to domain scientists. Given the ever-growing nature of these big data, we highlight key issues that big data integration methods will face.

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“…Compared with our previous study [28], we here introduced miRNA expression profiles to gain insights into the biological effects of small molecules and miRNAs more deeply in this study. The workflow of our approach is shown in the electronic supplementary material, figure S1.…”

Section: Discussionmentioning

confidence: 99%

“…Our previous research investigated the potential connections between small molecules and miRNAs across 23 human cancers based on transcriptional responses similarity. We constructed a complex small molecule and miRNA network among 23 cancers and explored the molecular and functional features for small molecule modules, as well as miRNA modules in each cancer type [28].…”

Section: Introductionmentioning

confidence: 99%

Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease

Meng

Dai

et al. 2014

J. R. Soc. Interface.

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Alzheimer's disease (AD) is an incurable neurodegenerative disorder. Much effort has been devoted to developing effective therapeutic agents. Recently, targeting microRNAs (miRNAs) with small molecules has become a novel therapy for human diseases. In this study, we present a systematic computational approach to construct a bioactive Small molecule and miRNA association Network in AD (SmiRN-AD), which is based on the gene expression signatures of bioactive small molecule perturbation and AD-related miRNA regulation. We also performed topological and functional analysis of the SmiRN-AD from multiple perspectives. At the significance level of p ≤ 0.01, 496 small molecule–miRNA associations, including 25 AD-related miRNAs and 275 small molecules, were recognized and used to construct the SmiRN-AD. The drugs that were connected with the same miRNA tended to share common drug targets ( p = 1.72 × 10 −4 ) and belong to the same therapeutic category ( p = 4.22 × 10 −8 ). The miRNAs that were linked to the same small molecule regulated more common miRNA targets ( p = 6.07 × 10 −3 ). Further analysis of the positive connections (quinostatin and miR-148b, amantadine and miR-15a) and the negative connections (melatonin and miR-30e-5p) indicated that our large-scale predictions afforded specific biological insights into AD pathogenesis and therapy. This study proposes a holistic strategy for deciphering the associations between small molecules and miRNAs in AD, which may be helpful for developing a novel effective miRNA-associated therapeutic strategy for AD. A comprehensive database for the SmiRN-AD and the differential expression patterns of the miRNA targets in AD is freely available at http://bioinfo.hrbmu.edu.cn/SmiRN-AD/ .

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Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses

Cited by 68 publications

References 54 publications

A review of connectivity map and computational approaches in pharmacogenomics

A review of connectivity map and computational approaches in pharmacogenomics

Integrative methods for analyzing big data in precision medicine

Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease

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