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Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer

Paola Paci, Teresa Colombo, Lorenzo Farina
2014 BMC Systems Biology  
We built normal and cancer networks of miRNA-mediated sponge interactions (MMI-networks) using breast cancer expression data provided by The Cancer Genome Atlas.  ...  This variegated class of RNA species encompasses the well-known microRNAs (miRNAs) and the most recently acknowledged long non-coding RNAs (lncRNAs).  ...  Acknowledgments The authors thank CINECA for the computational support, Prof. G. Macino for encouragement and fresh biological insights and Dr. A.  ... 
doi:10.1186/1752-0509-8-83 pmid:25033876 pmcid:PMC4113672 fatcat:dgi4vu2anrb5lb5dowumevcmwa

SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks

Paola Paci, Giulia Fiscon
2022 BMC Bioinformatics  
PVT1, a long non-coding RNA functioning as ceRNA for the miR-200 family.  ...  Background Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions.  ...  Then, SPINNAKER separates the two selected classes of candidate ceRNAs to be tested (e.g., protein coding versus long non-coding RNAs).  ... 
doi:10.1186/s12859-022-04695-x pmid:35524174 pmcid:PMC9073480 fatcat:ejsosekrrfesvdunbglyhmufju

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer

Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci, Turgay Unver
2017 PLoS ONE  
The ceRNAs are also called miRNA "decoys" or miRNA "sponges" and encompass different RNAs competing with each other to attract miRNAs for interactions: mRNA, long non-coding RNAs (lncRNAs), pseudogenes  ...  In particular, we focused on the withdrawal in breast cancer tissues of the PVT1 ceRNA activity and performed a gene expression and sequence analysis of its multiple isoforms.  ...  The authors thank Leandro Castellano-Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM)-for providing the RNA-seq raw data.  ... 
doi:10.1371/journal.pone.0171661 pmid:28187158 pmcid:PMC5302781 fatcat:fp6e25spszexjg62rc5n7eomni

Competing endogenous RNA networks in human cancer: hypothesis, validation, and perspectives

Chao Yang, Di Wu, Lin Gao, Xi Liu, Yinji Jin, Dong Wang, Tianzhen Wang, Xiaobo Li
2016 OncoTarget  
Non-coding RNAs represent a majority of the human transcriptome. However, less is known about the functions and regulatory mechanisms of most non-coding species.  ...  Here we review the evolution of the ceRNA hypothesis, summarize the validation experiments and discusses the significance and perspectives of this hypothesis in human cancer.  ...  LncrNAs as cerNAs in human cancer HULC is the first long non-coding RNA identified to be specifically and highly increased in HCC [58] .  ... 
doi:10.18632/oncotarget.7266 pmid:26872371 pmcid:PMC4924655 fatcat:kfguag6dsna7hhklfmokieqiq4

Noncoding RNA:RNA Regulatory Networks in Cancer

Jia Chan, Yvonne Tay
2018 International Journal of Molecular Sciences  
The different subclasses of ncRNAs include microRNAs, a class of short ncRNAs; and a variety of long ncRNAs (lncRNAs), such as lincRNAs, antisense RNAs, pseudogenes, and circular RNAs.  ...  This largest class of RNA transcripts plays diverse roles in a multitude of cellular processes, and has been implicated in many pathological conditions, especially cancer.  ...  Yvonne Tay was supported by a Singapore National Research Foundation Fellowship and a National University of Singapore President's Assistant Professorship.  ... 
doi:10.3390/ijms19051310 pmid:29702599 pmcid:PMC5983611 fatcat:ts5tkk52z5dulpt7nnvwm4nlqe

Stratification of lncRNA modulation networks in breast cancer

Wen-Hsuan Yu, Chia-Lang Hsu, Chen-Ching Lin, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang
2021 BMC Medical Genomics  
Long non-coding RNAs (lncRNAs) are defined as non-protein coding transcripts longer than 200 nucleotides. We already knew that lncRNAs are related to cancers and will be dysregulated in them.  ...  Conclusions We proposed a modulatory analysis to infer the ceRNA effects among mRNAs and lncRNAs and performed functional analysis to reveal the plausible mechanisms of lncRNA modulation in the four breast  ...  Bioinformatics, National Taiwan University, Taipei, Taiwan. 2 Center for Computational and Systems Biology, National Taiwan University, Taipei, Taiwan. 3 Institute of Biomedical Informatics, National  ... 
doi:10.1186/s12920-022-01236-6 pmid:35501896 pmcid:PMC9059351 fatcat:cq57wcratnc27pijxbxpsh3wpm

Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers

Dulari K. Jayarathna, Miguel E. Rentería, Emilie Sauret, Jyotsna Batra, Neha S. Gandhi
2021 Biology  
We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across five HD cancers.  ...  Here, we identify an extended ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of five hormone-dependent (HD) cancers, i.e., prostate, breast, colon, rectal, and  ...  The computational resources and services used in this work were provided by the eResearch Office, Queensland University of Technology, Brisbane, Australia.  ... 
doi:10.3390/biology10101014 pmid:34681112 fatcat:locz5m745fhg5d3goy4idyzucy

miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions

Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo, Alfonso Urso
2020 BMC Bioinformatics  
Non-coding RNAs include different classes of molecules with regulatory functions.  ...  They behave as competitive endogenous RNA (ceRNA), acting as natural miRNA sponges to inhibit miRNA functions and modulate the expression of RNA messenger (mRNA).  ...  Acknowledgements The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www. cancer.gov/tcga. About this supplement  ... 
doi:10.1186/s12859-020-3520-z pmid:32938402 pmcid:PMC7493844 fatcat:abwpgnafxnfdtabbmo4ugd6ema

Computational Models in Non-Coding RNA and Human Disease

Xing Chen, Chun-Chun Wang, Na-Na Guan
2020 International Journal of Molecular Sciences  
The central dogma of molecular biology has told that DNA sequences encode proteins through RNAs, which function as an information intermediary [...]  ...  [38] incorporated several datasets, including circRNA, mRNA, miRNA and pathway data to design a non-negative matrix factorization-based model for identifying breast cancer-related circRNA modules.  ...  Based on the transcript length and structure, ncRNAs can be divided into different classes, including microRNA (miRNA), long non-coding RNA (lncRNA), transcribed ultraconserved regions (T-UCRs), small  ... 
doi:10.3390/ijms21051557 pmid:32106478 pmcid:PMC7084754 fatcat:xrznrhgpxzcyxizcr3euvaqnzm

Interaction and cross-talk between non-coding RNAs

Soichiro Yamamura, Mitsuho Imai-Sumida, Yuichiro Tanaka, Rajvir Dahiya
2017 Cellular and Molecular Life Sciences (CMLS)  
Long non-coding RNAs (lncR-NAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites.  ...  LncRNAs are transcribed RNA molecules longer than 200 nucleotides and lncRNA transcripts account for a large proportion of the non-coding transcriptome [1] [2] [3] .  ...  Computational analysis of lncRNA-miRNA interaction There have been a number of reports that demonstrate lncRNA-miRNA interaction identified by computational or data analysis ( Table 2 ).  ... 
doi:10.1007/s00018-017-2626-6 pmid:28840253 pmcid:PMC5765200 fatcat:iswkollzw5aehckexpah6mspbu

Competing endogenous RNA networks: tying the essential knots for cancer biology and therapeutics

Avencia Sanchez-Mejias, Yvonne Tay
2015 Journal of Hematology & Oncology  
Recent reports have implicated diverse RNA species including protein-coding messenger RNAs and non-coding RNAs as ceRNAs in human development and diseases including human cancer.  ...  In this review, we discuss the most recent discoveries that implicate natural miRNA decoys in human cancer biology, as well as exciting advances in the study of ceRNA networks and dynamics.  ...  Y.T. was supported by a Singapore National Research Foundation Fellowship and a National University of Singapore President's Assistant Professorship. Received: 9 December 2014 Accepted: 16 March 2015  ... 
doi:10.1186/s13045-015-0129-1 pmid:25888444 pmcid:PMC4381443 fatcat:sa2szb7vpbgqdfh4du3n2agms4

Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer

Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
2017 BMC Bioinformatics  
We focus on investigating breast cancer (BRCA) related miRNA sponge co-regulation, by integrating heterogeneous data, including miRNA, long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression data  ...  Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers.  ...  Availability of data and materials The datasets and source code in the current study are available at https://github.com/ zhangjunpeng411/miRSCoPPI.  ... 
doi:10.1186/s12859-017-1672-2 pmid:28482794 pmcid:PMC5423010 fatcat:66h3izqt4regfcxj3mm4g5t6ku

Non-Coding RNAs and their Integrated Networks

Peijing Zhang, Wenyi Wu, Qi Chen, Ming Chen
2019 Journal of Integrative Bioinformatics  
As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins.  ...  Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes.  ...  All authors have read the journal's publication ethics and publication malpractice statement available at the journal's website and hereby confirm that they comply with all its parts applicable to the  ... 
doi:10.1515/jib-2019-0027 pmid:31301674 pmcid:PMC6798851 fatcat:de5a42jvnzd2zjvirxiczyjp2m

The multilayered complexity of ceRNA crosstalk and competition

Yvonne Tay, John Rinn, Pier Paolo Pandolfi
2014 Nature  
RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs.  ...  RNA crosstalk in competitive endogenous networks Competition between various molecular species to bind to a specific molecular target has been described in multiple contexts, and includes DNA-protein,  ...  Recent reports indicate that aside from around 21,000 protein-coding genes, the human transcriptome includes about 9,000 small RNAs, about 10,000-32,000 long non-coding RNAs (lncRNAs) and around 11,000  ... 
doi:10.1038/nature12986 pmid:24429633 pmcid:PMC4113481 fatcat:5vmwh5i4szambczphmnl7repti

Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine

Giulia Fiscon, Federica Conte, Lorenzo Farina, Paola Paci
2018 Genes  
In fact, there is a pool of different RNAs—including long non-coding RNAs (lncRNAs) —competing with each other to attract microRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs).  ...  The past few years have witnessed the increasing interest in understanding the molecular mechanism of post-transcriptional regulation with a special emphasis on non-coding RNAs since they are emerging  ...  Recently, a computational method [25] was developed for identifying putative lncRNAs acting as miRNAs sponges in human breast cancer.  ... 
doi:10.3390/genes9090437 pmid:30200360 pmcid:PMC6162385 fatcat:hkrmpxhfizbbjcdtdhxdrhfzd4
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