ArticleBMC bioinformatics2010
Gene bi-targeting by viral and human miRNAs.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Essential role of hsa-miR-203a-3p in type I interferons immune homeostasis during influenza and NDV infection.RNA biology · 2026Article
- Epstein-Barr virus-encoded EBNA2 downregulates ICOSL by inducing miR-24 in B-cell lymphoma.Blood · 2024Article
- MirDIP 5.2: tissue context annotation and novel microRNA curation.Nucleic acids research · 2023Article
- Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA.Cell reports · 2022Article
- Regional and temporal miRNAs expression profile in a transgenic mouse model of tauopathy: implication for its pathogenesis.Molecular psychiatry · 2021Article
- Mechanism of bone marrow mesenchymal stem cells secreting miR-26a exosomes affecting high glucose-induced skin fibroblasts function by regulating TLR4/NF-κB signaling.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2021Article
- MicroRNAs in ascending thoracic aortic aneurysms.Bioscience reports · 2020Observational
- RPmirDIP: Reciprocal Perspective improves miRNA targeting prediction.Scientific reports · 2020Article
- Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2.PloS one · 2020Article
- mirDIP 4.1-integrative database of human microRNA target predictions.Nucleic acids research · 2018Article
- Article
- Increased Expression of Herpes Virus-Encoded hsv1-miR-H18 and hsv2-miR-H9-5p in Cancer-Containing Prostate Tissue Compared to That in Benign Prostate Hyperplasia Tissue.International neurourology journal · 2016Article
- Bioinformatic tools for microRNA dissection.Nucleic acids research · 2016Review
- An ensemble approach to the evolution of complex systems.Journal of biosciences · 2014Review
- Epigenetic silencing of miR-375 induces trastuzumab resistance in HER2-positive breast cancer by targeting IGF1R.BMC cancer · 2014Article
- RNA viruses and microRNAs: challenging discoveries for the 21st century.Physiological genomics · 2013Review
- Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV).BMC bioinformatics · 2012Article
- The miRNAs of herpes simplex virus (HSV).Virologica Sinica · 2012Review
- MicroRNAs in HIV-1 infection: an integration of viral and cellular interaction at the genomic level.Frontiers in microbiology · 2012Article
- Functional similarity analysis of human virus-encoded miRNAs.Journal of clinical bioinformatics · 2011Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (miRNAs) are an abundant class of small noncoding RNAs (20-24 nts) that can affect gene expression by post-transcriptional regulation of mRNAs. They play important roles in several biological processes (e.g., development and cell cycle regulation). Numerous bioinformatics methods have been developed to identify the function of miRNAs by predicting their target mRNAs. Some viral organisms also encode miRNAs, a fact that contributes to the complex interactions between viruses and their hosts. A need arises to understand the functional relationship between viral and host miRNAs and their effect on viral and host genes. Our approach to meet this challenge is to identify modules where viral and host miRNAs cooperatively regulate host gene expression.
resultsWe present a method to identify groups of viral and host miRNAs that cooperate in post-transcriptional gene regulation, and their target genes that are involved in similar biological processes. We call these groups (genes and miRNAs of human and viral origin) - modules. The modules are found in a new two-stage procedure, which we call bi-targeting, and is presented in this paper. The stages are (i) a new and efficient target prediction, and (ii) a new method for clustering objects of three different data types. In this work we integrate multiple information sources, including miRNA-target binding information, miRNA expression profiles, and GO annotations. Our hypotheses and the methods have been tested on human and Epstein Barr virus (EBV) miRNAs and human genes, for which we found 34 modules. We provide supporting evidence from biological and medical literature for two of our modules. Our code and data are available at http://www.cs.bgu.ac.il/~vaksler/BiTargeting.htm
conclusionsThe presented algorithm, which makes use of diverse biological data, is demonstrated to be an efficient approach for finding bi-targeting modules of viral and human miRNAs. These modules can contribute to a better understanding of viral-host interactions and the role that miRNAs play in them.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.