Erratum: Optimal scaling of digital transcriptomes (PLoS ONE (2013) 8:11 (e77885) DOI:10.1371/journal.pone.0077885);Optimal scaling of digital transcriptomes

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Glusman, Gustavo ^a   Caballero, Juan ^b   Robinson, Max ^a   Kutlu, Burak ^a   Hood, Leroy ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSIDAD AUTÓNOMA DE QUERÉTARO   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CONTROLLED STUDY; GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE TECHNOLOGY; GENETIC ALGORITHM; HOUSEKEEPING GENE; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCALE UP; TAXONOMIC IDENTIFICATION; UBIQUITOUS GENE;

ALGORITHMS; CALIBRATION; GENE EXPRESSION PROFILING; GENES, ESSENTIAL; GENOMICS; HUMANS; REFERENCE STANDARDS; SEQUENCE ANALYSIS, RNA; STATISTICS, NONPARAMETRIC; TRANSCRIPTOME;

EID: 84892380814     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093244     Document Type: Erratum

References (35)

1. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
2. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484-487.
3. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634.
4. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
5. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
6. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res 20: 180-189.
7. Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, et al. (2010) Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res 20: 1730-1739.
8. Lee S, Seo CH, Lim B, Yang JO, Oh J, et al. (2011) Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. Nucleic Acids Res 39: e9.
9. Zheng W, Chung LM, Zhao H (2011) Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics 12: 290.
10. Risso D, Schwartz K, Sherlock G, Dudoit S (2011) GC-content normalization for RNA-Seq data. BMC Bioinformatics 12: 480.
11. Shmulevich I, Zhang W (2002) Binary analysis and optimization-based normalization of gene expression data. Bioinformatics 18: 555-565.
12. Robinson M, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25.
13. Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, et al. (2004) The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res 14: 1641-1653.
14. de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, et al. (2005) Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest 85: 154-159.
15. Loven J, Orlando DA, Sigova AA, Lin CY, Rahl PB, et al. (2012) Revisiting global gene expression analysis. Cell 151: 476-482.
16. Bullard J, Purdom E, Hansen K, Dudoit S (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94.
17. Bolstad B, Irizarry R, Astrand M, Speed T (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
18. Mar J, Kimura Y, Schroder K, Irvine K, Hayashizaki Y, et al. (2009) Datadriven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics 10: 110.
19. Qiu X, Wu H, Hu R (2013) The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis. BMC Bioinformatics 14: 124.
20. Hansen KD, Irizarry RA, Wu Z (2012) Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13: 204-216.
21. Zhou L, Lim QE, Wan G, Too HP (2010) Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells. BMC Genomics 11: 75.
22. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: RESEARCH0034.
23. Hartemink AJ, Gifford DK, Jaakkola TS, Young RA (2001) Maximum likelihood estimation of optimal scaling factors for expression array normalization. SPIE BIOS 2001, San Jose, California, January 2001.
24. Sîrbu A, Ruskin HJ, Crane M (2010) Cross-Platform Microarray Data Normalisation for Regulatory Network Inference. PLoS ONE 5: e13822.
25. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
26. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
27. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
28. Kadota K, Nishiyama T, Shimizu K (2012) A normalization strategy for comparing tag count data. Algorithms Mol Biol 7: 5.
29. Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, et al. (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 15: 1007-1014.
30. Brin S, Page L (1998) The anatomy of a large-scale hyper-textual Web search engine. Computer Networks and ISDN Systems 30: 107-117.
31. Beyer H-G, Schwefel H-P (2002) Evolution strategies - A comprehensive introduction. Natural Computing 1: 3-52.
32. Zhu J, He F, Song S, Wang J, Yu J (2008) How many human genes can be defined as housekeeping with current expression data? BMC Genomics 9: 172.
33. Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, et al. (2012) A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform.
34. Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS (2004) Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A 101: 6559-6563.
35. Yang L, Xu L, He L (2009) A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction. Bioinformatics 25: 2244-2250.