Optimizing a Massive Parallel Sequencing workflow for quantitative miRNA expression analysis

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Cordero, Francesca ^a   Beccuti, Marco ^a   Arigoni, Maddalena ^a   Donatelli, Susanna ^a   Calogero, Raffaele A ^a  

^a UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE DUPLICATION; GENE EXPRESSION; GENE MAPPING; GENE TECHNOLOGY; GENETIC DATABASE; GENOME ANALYSIS; HUMAN; HUMAN CELL; MASSIVE PARALLEL SEQUENCING; PERIPHERAL BLOOD MONONUCLEAR CELL; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; SEGMENTATION ALGORITHM; SENSITIVITY AND SPECIFICITY; WORKFLOW; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; METABOLISM; METHODOLOGY; SAMPLE SIZE; SEQUENCE ALIGNMENT; STANDARD;

ALGORITHMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; REFERENCE STANDARDS; ROC CURVE; SAMPLE SIZE; SEQUENCE ALIGNMENT; SOFTWARE; WORKFLOW;

EID: 84857377692     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031630     Document Type: Article

References (34)

1. Willenbrock H, Salomon J, Sokilde R, Barken KB, Hansen TN, et al. (2009) Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA 15: 2028-2034.
2. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158.
3. Jayaprakash AD, Jabado O, Brown BD, Sachidanandam R, (2011) Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res.
4. Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, et al. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res 21: 1506-1511.
5. Zheng W, Chung LM, Zhao H, (2011) Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics 12: 290.
6. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, et al. (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 5: e1000386.
7. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. (2003) A uniform system for microRNA annotation. RNA 9: 277-279.
8. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
9. Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, et al. (2009) miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 10: 328.
10. Emde AK, Grunert M, Weese D, Reinert K, Sperling SR, (2010) MicroRazerS: rapid alignment of small RNA reads. Bioinformatics 26: 123-124.
11. Ronen R, Gan I, Modai S, Sukacheov A, Dror G, et al. (2010) miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics 26: 2615-2616.
12. Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, et al. (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 24: 2252-2253.
13. Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM, (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 37: W68-76.
14. Smedley D, Haider S, Ballester B, Holland R, London D, et al. (2009) BioMart-biological queries made easy. BMC Genomics 10: 22.
15. Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
16. Hardcastle TJ, Kelly KA, (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422.
17. Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
18. Wang L, Feng Z, Wang X, Zhang X, (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
19. Tusher VG, Tibshirani R, Chu G, (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
20. Breitling R, Armengaud P, Amtmann A, Herzyk P, (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573: 83-92.
21. Metz CE, (1978) Basic principles of ROC analysis. Semin Nucl Med 8: 283-298.
22. Sanges R, Cordero F, Calogero RA, (2007) oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Bioinformatics 23: 3406-3408.
23. Della Beffa C, Cordero F, Calogero RA, (2008) Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays. BMC Genomics 9: 571.
24. Morgan M, Anders S, Lawrence M, Aboyoun P, Pages H, et al. (2009) ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25: 2607-2608.
25. Califano A, Rigoutsos I, (1993) FLASH: a fast look-up algorithm for string homology. Proc Int Conf Intell Syst Mol Biol 1: 56-64.
26. Rasmussen KR, Stoye J, Myers EW, (2006) Efficient q-gram filters for finding all epsilon-matches over a given length. J Comput Biol 13: 296-308.
27. Farrar M, (2007) Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics 23: 156-161.
28. Weese D, Emde AK, Rausch T, Doring A, Reinert K, (2009) RazerS-fast read mapping with sensitivity control. Genome Res 19: 1646-1654.
29. Pasaniuc B, Zaitlen N, Halperin E, (2011) Accurate estimation of expression levels of homologous genes in RNA-seq experiments. J Comput Biol 18: 459-468.
30. Prufer K, Stenzel U, Dannemann M, Green RE, Lachmann M, et al. (2008) PatMaN: rapid alignment of short sequences to large databases. Bioinformatics 24: 1530-1531.
31. Bullard JH, Purdom E, Hansen KD, Dudoit S, (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94.
32. Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11: 237.
33. Robinson MD, Oshlack A, (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25.
34. Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.