Computational developments in microRNA-regulated protein-protein interactions

Zhu, Wei; Chen, Yi‐Ping Phoebe

doi:10.1186/1752-0509-8-14

Cited by 11 publications

(9 citation statements)

References 101 publications

(104 reference statements)

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“…In order to better address this topic, in the present study, the authors depicted an miRNA-mRNA interaction network through use of publicly accessible databases based around high-throughput screening data ( 6 ). It has been hypothesized that the interaction network between miRNA and mRNA associated with IPF may provide a novel approach for the determination of gene functions and mechanisms involved in the pathogenesis of IPF.…”

Section: Introductionmentioning

confidence: 99%

Molecular pathogenesis involved in human idiopathic pulmonary fibrosis based on an integrated microRNA‑mRNA interaction network

et al. 2018

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Idiopathic pulmonary fibrosis (IPF) is considered to be an ailment of the lungs that cannot be cured, wherein the lung tissues are characterized by increased thickness and stiffness, and/or scars. Despite the fact that extensive success has been achieved regarding the molecular diagnostics and pathobiology, the basic pathogenesis associated with IPF has not yet been fully elucidated and requires further clarification. In the current research, the changes in microRNA (miRNA) and mRNA expression in IPF were investigated through an integrative network technique. The authentic miRNA and mRNA expression profiling datasets were downloaded from Gene Expression Omnibus, followed by identification of differentially expressed miRNAs and mRNAs with use of the Significance Analysis of Microarrays algorithm. Expansion of the molecular targets associated with miRNAs was performed with the use of CyTargetLinker in Cytoscape, which was succeeded by validation with the use of mRNA array expression profiling. The incorporated miRNA-mRNA network covered 27 genes, in addition to 22 miRNAs that were associated with IPF development. As revealed by the functional enrichment analysis, the cytokine-cytokine receptor interaction and glycine, serine and threonine metabolism signalling pathways were extensively associated with IPF development. Overall, the present incorporated network illustrated the key link between miRNA and genes in IPF; in particular, it was elucidated that miR-409-5p and has-miR-376c, together with their target genes (C-C motif chemokine ligand 20 and oncostatin M), are likely candidates involved in the promotion of IPF initiation and progression.

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Section: Introductionmentioning

confidence: 99%

Molecular pathogenesis involved in human idiopathic pulmonary fibrosis based on an integrated microRNA‑mRNA interaction network

et al. 2018

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“…As is shown, mir-10 family prefers to target proteins of “PF00757: Furin-like” and “PF01030: Recep_L_domain” families, mir-17 family prefers to target proteins of “PF02234: Cyclin-dependent kinase inhibitor” and mir-34 family prefers to target proteins of “PF01056: Myc_N” and “PF00452: Bcl-2” family. As is known, miRNAs of the same family share conserved seed regions in their 5′ ends that play important role in specifically binding to mRNA targets, so miRNAs of the same family possibly share targets of the same protein family or in the same pathway 5 34 . Our work made a validation of the functional coordination of these miRNAs.…”

Section: Discussionmentioning

confidence: 99%

“…Most products of these mRNAs are essential proteins such as signaling proteins, enzymes and transcription factors (TFs) that are involved in various cellular processes. Most of these proteins have been proved to be hub or bottleneck proteins in human protein-protein interaction network (PPIN) 5 . In this case, aberrant miRNA regulation would lead to a dynamic change in human PPIN, thus to activate or inhibit some signaling pathways related to diseases even cancers 6 7 .…”

mentioning

confidence: 99%

Dissecting the regulation rules of cancer-related miRNAs based on network analysis

Liu

Guo

et al. 2016

Sci Rep

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miRNAs (microRNAs) are a set of endogenous and small non-coding RNAs which specifically induce degradation of target mRNAs or inhibit protein translation to control gene expression. Obviously, aberrant miRNA expression in human cells will lead to a serious of changes in protein-protein interaction network (PPIN), thus to activate or inactivate some pathways related to various diseases, especially carcinogenesis. In this study, we systematically constructed the miRNA-regulated co-expressed protein-protein interaction network (CePPIN) for 17 cancers firstly. We investigated the topological parameters and functional annotation for the proteins in CePPIN, especially for those miRNA targets. We found that targets regulated by more miRNAs tend to play a more important role in the forming process of cancers. We further elucidated the miRNA regulation rules in PPIN from a more systematical perspective. By GO and KEGG pathway analysis, miRNA targets are involved in various cellular processes mostly related to cell cycle, such as cell proliferation, growth, differentiation, etc. Through the Pfam classification, we found that miRNAs belonging to the same family tend to have targets from the same family which displays the synergistic function of these miRNAs. Finally, the case study on miR-519d and miR-21-regulated sub-network was performed to support our findings.

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“…Deregulation of enzymes and cofactors involved in these pathways [16,17] can affect the levels of mature miRNAs and have important biological ramifications. Hence, the study of interaction mechanism between miRNAs and their target genes is essential.…”

Section: Discussionmentioning

confidence: 99%

Study of miRNA based gene regulation involved in Squamous Lung Carcinoma by assistance of Argonaute Protein

Chandra¹,

Kumar²,

Khan³

2018

IJRDPL

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miRNAs are responsible for gene silencing and has functions in various diseases like cancer. miRNAs are responsible for cancer and at the same time act as tumor suppressors. The work mentioned here is based on study on differentially expressed miRNAs for squamous cell carcinoma target genes in the metabolic pathways. The study focused on combination of miRNA and their target genes for squamous cell carcinoma as well as how they are involved in metabolic pathways. miRNAs were categorized into normal, up-regulated and down-regulated genes. Prediction of target genes for miRNAs followed by developing a relationship between them was done. miRNA target genes involved in metabolic pathways which were studied for squamous lung carcinoma. miRNA target genes were doc ked with argonaute protein. Docking was done in order to understand how miRNA tend to bind to target gene. Results added information to the study of how miRNAs targets genes in various metabolic pathways. The expression level of miRNA is different in diffe rent conditions which can be modified as a result of defects in the miRNA biogenesis pathway.

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Computational developments in microRNA-regulated protein-protein interactions

Cited by 11 publications

References 101 publications

Molecular pathogenesis involved in human idiopathic pulmonary fibrosis based on an integrated microRNA‑mRNA interaction network

Molecular pathogenesis involved in human idiopathic pulmonary fibrosis based on an integrated microRNA‑mRNA interaction network

Dissecting the regulation rules of cancer-related miRNAs based on network analysis

Study of miRNA based gene regulation involved in Squamous Lung Carcinoma by assistance of Argonaute Protein

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