Literature DB >> 20560041

Toward understanding the informatics and statistical aspects of micro-RNA profiling.

Aaron L Sarver1.   

Abstract

Understanding of the role of micro-RNA (miRNA) in multicellular life has blossomed in the end of the first decade of the twenty-first century. Currently, miRNA-mediated control of development and pathogenesis is potentially approaching a level of importance equivalent to traditional transcriptional and translational controls. Due to the rapid spread of miRNA-profiling experiments and the possible value of information that is obtainable by these type of experiments, it is a punctual moment to step back and review (1) technologies available for determining the levels of miRNA present in a biological sample including microarray, bead, and quantitative sequencing-based approaches; (2) aspects regarding the quality and the normalization of profiling data; and (3) the statistical and bioinformatics analyses of miRNA profiling experiments. It is the hope of the author that this review will shed light on both the opportunities available to the researcher and the potential pitfalls that exist in this frontier of biomedical research.

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Year:  2010        PMID: 20560041     DOI: 10.1007/s12265-010-9180-z

Source DB:  PubMed          Journal:  J Cardiovasc Transl Res        ISSN: 1937-5387            Impact factor:   4.132


  19 in total

1.  Global analysis of protein localization in budding yeast.

Authors:  Won-Ki Huh; James V Falvo; Luke C Gerke; Adam S Carroll; Russell W Howson; Jonathan S Weissman; Erin K O'Shea
Journal:  Nature       Date:  2003-10-16       Impact factor: 49.962

2.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors:  B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

3.  Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.

Authors:  Christopher K Raymond; Brian S Roberts; Phillip Garrett-Engele; Lee P Lim; Jason M Johnson
Journal:  RNA       Date:  2005-11       Impact factor: 4.942

4.  RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.

Authors:  Fangxin Hong; Rainer Breitling; Connor W McEntee; Ben S Wittner; Jennifer L Nemhauser; Joanne Chory
Journal:  Bioinformatics       Date:  2006-09-18       Impact factor: 6.937

5.  MicroRNA expression profiles classify human cancers.

Authors:  Jun Lu; Gad Getz; Eric A Miska; Ezequiel Alvarez-Saavedra; Justin Lamb; David Peck; Alejandro Sweet-Cordero; Benjamin L Ebert; Raymond H Mak; Adolfo A Ferrando; James R Downing; Tyler Jacks; H Robert Horvitz; Todd R Golub
Journal:  Nature       Date:  2005-06-09       Impact factor: 49.962

6.  Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues.

Authors:  Heidi J Peltier; Gary J Latham
Journal:  RNA       Date:  2008-03-28       Impact factor: 4.942

7.  A mammalian microRNA expression atlas based on small RNA library sequencing.

Authors:  Pablo Landgraf; Mirabela Rusu; Robert Sheridan; Alain Sewer; Nicola Iovino; Alexei Aravin; Sébastien Pfeffer; Amanda Rice; Alice O Kamphorst; Markus Landthaler; Carolina Lin; Nicholas D Socci; Leandro Hermida; Valerio Fulci; Sabina Chiaretti; Robin Foà; Julia Schliwka; Uta Fuchs; Astrid Novosel; Roman-Ulrich Müller; Bernhard Schermer; Ute Bissels; Jason Inman; Quang Phan; Minchen Chien; David B Weir; Ruchi Choksi; Gabriella De Vita; Daniela Frezzetti; Hans-Ingo Trompeter; Veit Hornung; Grace Teng; Gunther Hartmann; Miklos Palkovits; Roberto Di Lauro; Peter Wernet; Giuseppe Macino; Charles E Rogler; James W Nagle; Jingyue Ju; F Nina Papavasiliou; Thomas Benzing; Peter Lichter; Wayne Tam; Michael J Brownstein; Andreas Bosio; Arndt Borkhardt; James J Russo; Chris Sander; Mihaela Zavolan; Thomas Tuschl
Journal:  Cell       Date:  2007-06-29       Impact factor: 41.582

8.  Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot.

Authors:  Gurman Singh Pall; Carles Codony-Servat; Jane Byrne; Leigh Ritchie; Andrew Hamilton
Journal:  Nucleic Acids Res       Date:  2007-04-02       Impact factor: 16.971

9.  Identification by Real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumoral tissues.

Authors:  E Bandrés; E Cubedo; X Agirre; R Malumbres; R Zárate; N Ramirez; A Abajo; A Navarro; I Moreno; M Monzó; J García-Foncillas
Journal:  Mol Cancer       Date:  2006-07-19       Impact factor: 27.401

10.  Muscle-specific microRNA miR-206 promotes muscle differentiation.

Authors:  Hak Kyun Kim; Yong Sun Lee; Umasundari Sivaprasad; Ankit Malhotra; Anindya Dutta
Journal:  J Cell Biol       Date:  2006-08-21       Impact factor: 10.539

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  12 in total

1.  Perturbation of 14q32 miRNAs-cMYC gene network in osteosarcoma.

Authors:  Venugopal Thayanithy; Aaron L Sarver; Reena V Kartha; Lihua Li; Andrea Y Angstadt; Matthew Breen; Clifford J Steer; Jaime F Modiano; Subbaya Subramanian
Journal:  Bone       Date:  2011-10-18       Impact factor: 4.398

2.  miRNAs differentially expressed by next-generation sequencing in cord blood buffy coat samples of boys and girls.

Authors:  Daneida Lizarraga; Karen Huen; Mary Combs; Maria Escudero-Fung; Brenda Eskenazi; Nina Holland
Journal:  Epigenomics       Date:  2016-11-24       Impact factor: 4.778

3.  Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma.

Authors:  David A Largaespada; Jaime F Modiano; Subbaya Subramanian; Milcah C Scott; Nuri A Temiz; Anne E Sarver; Rebecca S LaRue; Susan K Rathe; Jyotika Varshney; Natalie K Wolf; Branden S Moriarity; Timothy D O'Brien; Logan G Spector; Aaron L Sarver
Journal:  Cancer Res       Date:  2017-10-24       Impact factor: 12.701

4.  Studying microRNAs in the brain: technical lessons learned from the first ten years.

Authors:  Sébastien S Hébert; Peter T Nelson
Journal:  Exp Neurol       Date:  2011-12-08       Impact factor: 5.330

5.  Triptolide induces the expression of miR-142-3p: a negative regulator of heat shock protein 70 and pancreatic cancer cell proliferation.

Authors:  Tiffany N MacKenzie; Nameeta Mujumdar; Sulagna Banerjee; Veena Sangwan; Aaron Sarver; Selwyn Vickers; Subbaya Subramanian; Ashok K Saluja
Journal:  Mol Cancer Ther       Date:  2013-05-01       Impact factor: 6.261

6.  Retinoblastoma tumor cell proliferation is negatively associated with an immune gene expression signature and increased immune cells.

Authors:  Aaron L Sarver; Chencheng Xie; Megan J Riddle; Colleen L Forster; Xiaohong Wang; Huarui Lu; Wyatt Wagner; Jakub Tolar; Timothy C Hallstrom
Journal:  Lab Invest       Date:  2021-03-03       Impact factor: 5.662

7.  MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data.

Authors:  Guy N Brock; Partha Mukhopadhyay; Vasyl Pihur; Cynthia Webb; Robert M Greene; M Michele Pisano
Journal:  Source Code Biol Med       Date:  2013-01-08

Review 8.  Circulating microRNAs as biomarkers, therapeutic targets, and signaling molecules.

Authors:  Seena K Ajit
Journal:  Sensors (Basel)       Date:  2012-03-08       Impact factor: 3.576

9.  MicroRNA sequence profiles of human kidney allografts with or without tubulointerstitial fibrosis.

Authors:  Iddo Z Ben-Dov; Thangamani Muthukumar; Pavel Morozov; Franco B Mueller; Thomas Tuschl; Manikkam Suthanthiran
Journal:  Transplantation       Date:  2012-12-15       Impact factor: 4.939

10.  MicroRNAs at the human 14q32 locus have prognostic significance in osteosarcoma.

Authors:  Aaron L Sarver; Venugopal Thayanithy; Milcah C Scott; Anne-Marie Cleton-Jansen; Pancras Cw Hogendoorn; Jaime F Modiano; Subbaya Subramanian
Journal:  Orphanet J Rare Dis       Date:  2013-01-11       Impact factor: 4.123

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