A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-sample RNA-Seq Data

Statistics in Biosciences

Volumn 5, Issue 1, 2013, Pages 119-137

  Vardhanabhuti, Saran ^a   Li, Mingyao ^a   Li, Hongzhe ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Markov chain Monte Carlo sampling; Mixture of Poisson Gamma model; Next generation sequencing

Indexed keywords

RNA ISOFORM;

ACCURACY; ARTICLE; BAYES THEOREM; COVARIANCE; DATA ANALYSIS; GENE EXPRESSION; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; PRIORITY JOURNAL; RNA SEQUENCE; SIMULATION; STATISTICAL MODEL;

EID: 84877043834     PISSN: 18671764     EISSN: 18671772     Source Type: Journal    
DOI: 10.1007/s12561-011-9052-3     Document Type: Article

References (17)

1. Christiansen CL, Morris CN (1997) Hierarchical Poisson regression modeling. J Am Stat Assoc 92: 618-632.
2. Gilks WR (1992) Derivative-free adaptive rejection sampling for Gibbs sampling. In: Bayesian statistics, vol 4. Oxford University Press, London, pp 641-649.
3. Jiang H, Wong WH (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25: 1026-1032.
4. Kass R, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90: 773-795.
5. Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
6. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN (2009) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26: 493-500.
7. Li J, Jiang H, Wong WH (2010) Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol 11: R50.
8. 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.
9. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
10. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
11. Muller P, Parmigiani G, Rice K (2006) FDR and Bayesian multiple comparisons rules. In: Proc Valencia/ISBA 8th World meeting on Bayesian statistics, Benidorm, Alicante, Spain.
12. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
13. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard J (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
14. Spiegelhalter DJ, Thomas A, Best NG (1999) WinBUGS version 1. 2 user manual. MRC Biostatistics Unit.
15. Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, Akey JM (2007) Gene-expression variation within and among human populations. Am J Hum Genet 80: 502-509.
16. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
17. Zhang W, Duan S, Kistner EO, Bleibel WK, Huang RS, Clark TA, Chen TX, Schweitzer AC, Blume JE, Cox NJ, Dolan ME (2008) Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet 82: 631-640.