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Defining and providing robust controls for microRNA prediction

William Ritchie, Dadi Gao, John E. J. Rasko
2012 Bioinformatics  
The efficiency of these predictions relies on the set of positive and negative controls used.  ...  We demonstrate that commonly used positive and negative controls may be unreliable and provide a rational methodology with which to replace them.  ...  , we introduce a novel method to create a set of robust negative controls.  ... 
doi:10.1093/bioinformatics/bts114 pmid:22408193 fatcat:tcrhjfsyxncrxl5kum7zwrwofm

RSRE: RNA structural robustness evaluator

Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
2007 Nucleic Acids Research  
Biological robustness, defined as the ability to maintain stable functioning in the face of various perturbations, is an important and fundamental topic in current biology, and has become a focus of numerous  ...  Computational analysis results are needed to make up for the lack of evidence of robustness in natural biological systems.  ...  ACKNOWLEDGEMENTS The authors would like to thank the Super Biomed Computation Center at the Beijing Institute of Health Administration and Medicine Information for providing computing resources.  ... 
doi:10.1093/nar/gkm361 pmid:17567615 pmcid:PMC1933138 fatcat:52egluueknh53gtphaldagfk64

Tissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways

Andreas Kowarsch, Carsten Marr, Daniel Schmidl, Andreas Ruepp, Fabian J. Theis, Richard James Morris
2010 PLoS ONE  
Our analysis provides systematic insights into the interaction of disease-associated microRNAs and signaling pathways and uncovers differences in cellular locations and process types of microRNA targets  ...  They play a critical role in many cellular processes and have been linked to the control of signal transduction pathways.  ...  Acknowledgments We would like to thank Sebastian Bohl, Jan Krumsiek, and Florian Blöchl for stimulating remarks.  ... 
doi:10.1371/journal.pone.0011154 pmid:20614023 pmcid:PMC2894853 fatcat:uepsbg7nhnh27igfhfzvr7lrdi

Computational Analysis of mRNA Expression Profiles Identifies MicroRNA-29a/c as Predictor of Colorectal Cancer Early Recurrence

Tai-Yue Kuo, Edward Hsi, I-Ping Yang, Pei-Chien Tsai, Jaw-Yuan Wang, Suh-Hang Hank Juo, Steve Horvath
2012 PLoS ONE  
MicroRNAs may serve as biomarkers to predict early recurrence of CRC, but identifying them from over 1,400 known human microRNAs is challenging and costly.  ...  (p = 9.14610 29 for miR-29a and p = 1.14610 26 for miR-29c).  ...  Conceived and designed the experiments: TK SJ. Performed the experiments: TK IY. Analyzed the data: TK EH PT. Contributed reagents/materials/analysis tools: JW SJ. Wrote the paper: TK PT SJ.  ... 
doi:10.1371/journal.pone.0031587 pmid:22348113 pmcid:PMC3278467 fatcat:fig73kpxfvarjgaueisnsdboxi

Systematic functional characterization of cis-regulatory motifs in human core promoters

S. Sinha, A. S. Adler, Y. Field, H. Y. Chang, E. Segal
2008 Genome Research  
Our analysis also identifies many motifs whose target sets are predicted to be regulated by a common microRNA, suggesting a connection between transcriptional and post-transcriptional control processes  ...  Finally, we predict novel roles for uncharacterized motifs in the regulation of specific biological processes and certain types of human cancer, and experimentally validate four such predictions, suggesting  ...  Kaplan, and D. Pe'er for useful comments on the manuscript. A.S.A was supported by NCI, DHHS grant CA09302, and the California Breast Cancer Research Program.  ... 
doi:10.1101/gr.6828808 pmid:18256240 pmcid:PMC2259112 fatcat:czhrnj6stjeohgmg2ub5a3scha

Identification of a MicroRNA Panel for Clear-cell Kidney Cancer

David Juan, Gabriela Alexe, Travis Antes, Huiqing Liu, Anant Madabhushi, Charles Delisi, Shridhar Ganesan, Gyan Bhanot, Louis S. Liou
2010 Urology  
OBJECTIVES To identify a robust panel of microRNA signatures that can classify tumor from normal kidney using microRNA expression levels.  ...  Mounting evidence suggests that microRNAs are key players in essential cellular processes and that their expression pattern can serve as diagnostic biomarkers for cancerous tissues.  ...  Endogenous MicroRNA Reference Control For relative quantification, the normalization of each mi-croRNA expression is defined relative to endogenous control (housekeeping) microRNA with respect to each  ... 
doi:10.1016/j.urology.2009.10.033 pmid:20035975 fatcat:25faapuumnhzvmocy3wtg7eotq

Prioritization of disease microRNAs through a human phenome-microRNAome network

Qinghua Jiang, Yangyang Hao, Guohua Wang, Liran Juan, Tianjiao Zhang, Mingxiang Teng, Yunlong Liu, Yadong Wang
2010 BMC Systems Biology  
The identification of disease-related microRNAs is vital for understanding the pathogenesis of diseases at the molecular level, and is critical for designing specific molecular tools for diagnosis, treatment  ...  Conclusions: We presented a network-based approach that can infer potential microRNA-disease associations and drive testable hypotheses for the experimental efforts to identify the roles of microRNAs in  ...  algorithm. miR2Disease [38] and HMDD [39] databases provide comprehensive resources for microRNA deregulation in human disease.  ... 
doi:10.1186/1752-0509-4-s1-s2 pmid:20522252 pmcid:PMC2880408 fatcat:4ycz4tte6jadhap66gxx57cvzq

Computational methods for the identification of microRNA targets

Xiaofeng Zhou, Dai
2010 Open Access Bioinformatics  
The prediction of microRNA targets and detection of microRNA-mRNA regulatory modules (MRMs) are crucial components for understanding of microRNA functions.  ...  Numerous computational methods for microRNA target prediction have been developed.  ...  We thank Ms Katherine Long for her editorial assistance. The authors report no conflicts of interest in this work.  ... 
doi:10.2147/oab.s6902 pmid:22162940 pmcid:PMC3233190 fatcat:ycfiypd5vzc63ntdlm376a7yly

MicroRNA inhibition fine-tunes and provides robustness to the restriction point switch of the cell cycle

Ricardo C. H. del Rosario, Joseph Ray Clarence G. Damasco, Baltazar D. Aguda
2016 Scientific Reports  
Our mathematical analysis shows that microRNAs play an essential role in fine-tuning and providing robustness to the switch.  ...  The proper regulation of this switch is important for normal cell processes; aberrations could result in a number of diseases such as cancer, neurodegenerative disorders, stroke and myocardial infarction  ...  Acknowledgements We would like to acknowledge support from the Philippine Genome Center, University of the Philippines Diliman and the Office of the Vice President for Academic Affairs, University of the  ... 
doi:10.1038/srep32823 pmid:27610602 pmcid:PMC5017317 fatcat:7o522t3j4vd5nkpk3nkokv5ggi

MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells

Richard Moore, Hsu Kiang Ooi, Taek Kang, Leonidas Bleris, Lan Ma, Jorg Stelling
2015 PLoS Computational Biology  
Our study via modeling in combination with quantitative experiments provides new evidence on the role of microRNA-mediated positive feedback loops in conferring robustness to the system performance of  ...  While the molecular interactions among p53 and microRNAs have emerged, a systems-level understanding of the regulatory mechanism and the role of microRNAs-forming feedback loops with the p53 core remains  ...  A large robustness index defined in S2 Text predicts that the system's probability of sustaining stable oscillation under stochastic perturbations is relatively high.  ... 
doi:10.1371/journal.pcbi.1004653 pmid:26642352 pmcid:PMC4671655 fatcat:wrdvay4fuvawtdf2quwi22fhoy

NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs

Elize A. Shirdel, Wing Xie, Tak W. Mak, Igor Jurisica, Esteban Ballestar
2011 PLoS ONE  
We integrate prediction databases, compare predictions to in vitro data, and use cross-database predictions to model the microRNA:transcript interactome -referred to as the micronome -to study microRNA  ...  Since microRNA binding is sequence-based but possibly structure-specific, work in this area has resulted in multiple databases storing predicted microRNA:target relationships computed using diverse algorithms  ...  Smith for his assistance with our network figures and Milton R. S. Smith for being a baby who slept -for the first month anyway.  ... 
doi:10.1371/journal.pone.0017429 pmid:21364759 pmcid:PMC3045450 fatcat:riqohyacfrhfrgljrwivjfkiia

MicroRNA-99 Family Members Suppress Homeobox A1 Expression in Epithelial Cells

Dan Chen, Zujian Chen, Yi Jin, Dragan Dragas, Leitao Zhang, Barima S. Adjei, Anxun Wang, Yang Dai, Xiaofeng Zhou, Barbara Bardoni
2013 PLoS ONE  
for the miR-99 family.  ...  A comprehensive bioinformatics analysis using 12 different sequence-based microRNA target prediction algorithms revealed that 81 out of these 266 down-regulated transcripts are potential direct targets  ...  Thomas Tuschl from Rockefeller University for providing us with the pIRESneo-FLAG/HA-Ago2 expression vector through Addgene Inc. We thank Dr. Wendy Cerny for editorial assistance.  ... 
doi:10.1371/journal.pone.0080625 pmid:24312487 pmcid:PMC3849180 fatcat:xkldjbscl5bbveghor6pfiviia

The next thing in prognostic molecular markers: microRNA signatures of cancer

W. M. Grady, M. Tewari
2010 Gut  
Their identification of this panel of prognostic microRNAs for gastric cancer is one of several recent studies that have found this class of small noncoding RNAs to be useful for predicting the behavior  ...  Beyond the promise that microRNAs hold as candidate biomarkers for the early detection and management of cancer, there is also considerable excitement for the use of miRNAs as a novel class of therapeutic  ...  Acknowledgments This work was supported by funding from the Burroughs Wellcome Trust (WMG) and 2P30CA015704-35 (WMG) and a Damon Runyon-Rachleff Innovator Award (MT)  ... 
doi:10.1136/gut.2009.200022 pmid:20551450 pmcid:PMC3377960 fatcat:aea5vrq5m5fqzpbbucud55oksq

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data

Saveria Mazzara, Riccardo L. Rossi, Renata Grifantini, Simone Donizetti, Sergio Abrignani, Mauro Bombaci
2017 Scientific Reports  
Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic  ...  Moreover, it can be used to foresee the more likely outcome of the disease, monitor its progression and predict the response to a given therapy.  ...  We thank also Alessandra Perfetti and Fabio Martelli for assistance with and sharing of their DM1 serum microRNA profiling and validation datasets and Chris Tachibana for critical reading and initial copy  ... 
doi:10.1038/srep45477 pmid:28358118 pmcid:PMC5371980 fatcat:3lkxx6yna5d4xlifm4c2xa3hnu

microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes

Rory Blevins, Ludovica Bruno, Thomas Carroll, James Elliott, Antoine Marcais, Christina Loh, Arnulf Hertweck, Azra Krek, Nikolaus Rajewsky, Chang-Zheng Chen, Amanda G. Fisher, Matthias Merkenschlager (+1 others)
2015 PLoS Genetics  
The ability of microRNAs to render gene expression more uniform across mammalian cell populations may be important for normal development and for disease.  ...  Computational approaches, synthetic gene circuits and observations in model organisms predict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cell variability in the expression  ...  Marvin Jens for critical reading of the manuscript and Drs. Andrea Weisse and Carla Bosia for advice on computational modeling.  ... 
doi:10.1371/journal.pgen.1005020 pmid:25714103 pmcid:PMC4340958 fatcat:w37tba3o2vf6bngp6tek2gvvcm
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