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Oh S, Song S, Dasgupta N, et al. The analytical landscape of static and temporal dynamics in transcriptome data. Front Genet. 2014;5:35doi: 10.3389/fgene.2014.00035.
Oh, S., Song, S., Dasgupta, N., & Grabowski, G. (2014). The analytical landscape of static and temporal dynamics in transcriptome data. Frontiers in genetics, 535. https://doi.org/10.3389/fgene.2014.00035
Oh, Sunghee, et al. "The analytical landscape of static and temporal dynamics in transcriptome data." Frontiers in genetics vol. 5 (2014): 35. doi: https://doi.org/10.3389/fgene.2014.00035
Oh S, Song S, Dasgupta N, Grabowski G. The analytical landscape of static and temporal dynamics in transcriptome data. Front Genet. 2014 Feb 20;5:35. doi: 10.3389/fgene.2014.00035. eCollection 2014. PMID: 24600473; PMCID: PMC3929947.
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Front Genet. 2014 Feb 20;5:35. doi: 10.3389/fgene.2014.00035. eCollection 2014.

The analytical landscape of static and temporal dynamics in transcriptome data.

Frontiers in genetics

Sunghee Oh, Seongho Song, Nupur Dasgupta, Gregory Grabowski

Affiliations

  1. Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA.
  2. Department of Mathematical Sciences, McMicken College of Arts and Sciences, University of Cincinnati Cincinnati, OH, USA.

PMID: 24600473 PMCID: PMC3929947 DOI: 10.3389/fgene.2014.00035

Abstract

Interpreting gene expression profiles often involves statistical analysis of large numbers of differentially expressed genes, isoforms, and alternative splicing events at either static or dynamic spectrums. Reduced sequencing costs have made feasible dense time-series analysis of gene expression using RNA-seq; however, statistical methods in the context of temporal RNA-seq data are poorly developed. Here we will review current methods for identifying temporal changes in gene expression using RNA-seq, which are limited to static pairwise comparisons of time points and which fail to account for temporal dependencies in gene expression patterns. We also review recently developed very few number of temporal dynamic RNA-seq specific methods. Application and development of RNA-specific temporal dynamic methods have been continuously under the development, yet, it is still in infancy. We fully cover microarray specific temporal methods and transcriptome studies in initial digital technology (e.g., SAGE) between traditional microarray and new RNA-seq.

Keywords: RNA-seq; differential expression; gene expression; initial digital technology; microarray; static and temporal dynamics

References

  1. Science. 1998 Oct 23;282(5389):699-705 - PubMed
  2. Genome Biol. 2010;11(3):R35 - PubMed
  3. Cancer Inform. 2011;10:205-15 - PubMed
  4. Brief Bioinform. 2011 May;12(3):280-7 - PubMed
  5. Nat Rev Drug Discov. 2002 Dec;1(12):951-60 - PubMed
  6. Comput Biol Chem. 2007 Aug;31(4):265-74 - PubMed
  7. BMC Bioinformatics. 2005 May 13;6:117 - PubMed
  8. PLoS Comput Biol. 2007 Jun;3(6):e120 - PubMed
  9. Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):334-9 - PubMed
  10. J Biol Chem. 2002 Mar 29;277(13):11527-32 - PubMed
  11. Bioinformatics. 2011 Oct 1;27(19):2672-8 - PubMed
  12. PLoS Genet. 2008 Feb;4(2):e14 - PubMed
  13. Nat Biotechnol. 2010 May;28(5):511-5 - PubMed
  14. BMC Bioinformatics. 2010 Feb 18;11:94 - PubMed
  15. Science. 2012 Oct 19;338(6105):349-54 - PubMed
  16. Bioinformatics. 2006 Feb 15;22(4):507-8 - PubMed
  17. Genetics. 2010 Jun;185(2):405-16 - PubMed
  18. Science. 1941 Aug 29;94(2435):210-1 - PubMed
  19. Mol Biol Cell. 1999 Jun;10(6):1859-72 - PubMed
  20. Gene. 2002 Jun 26;293(1-2):21-31 - PubMed
  21. EURASIP J Bioinform Syst Biol. 2009;:683463 - PubMed
  22. Physiol Genomics. 2003 Apr 16;13(2):119-27 - PubMed
  23. Bioinformatics. 2006 Jan 15;22(2):251-2 - PubMed
  24. Nature. 2002 May 2;417(6884):78-83 - PubMed
  25. Bioinformatics. 2006 May 1;22(9):1096-102 - PubMed
  26. BMC Bioinformatics. 2007 Jul 02;8:233 - PubMed
  27. Urol Oncol. 2014 Apr;32(3):327-36 - PubMed
  28. BMC Bioinformatics. 2009 Sep 23;10:310 - PubMed
  29. Genomics. 2013 Oct;102(4):229-36 - PubMed
  30. Nat Biotechnol. 2004 May;22(5):535-46 - PubMed
  31. Bioinformatics. 2004 Feb 12;20(3):332-9 - PubMed
  32. Mol Microbiol. 2010 Apr;76(1):12-24 - PubMed
  33. Bioinformatics. 2001;17 Suppl 1:S22-9 - PubMed
  34. J Comput Biol. 2002;9(2):317-30 - PubMed
  35. Chem Senses. 1998 Dec;23(6):735-42 - PubMed
  36. Algorithms Mol Biol. 2012 Apr 05;7(1):5 - PubMed
  37. Am J Bot. 2012 Feb;99(2):248-56 - PubMed
  38. Bioinformatics. 2003 Sep 1;19(13):1628-35 - PubMed
  39. Genome Res. 2012 Mar;22(3):577-91 - PubMed
  40. Genome Biol. 2010;11(12):220 - PubMed
  41. Nat Rev Genet. 2012 Jul 18;13(8):552-64 - PubMed
  42. Bioinformatics. 2009 Jun 15;25(12):i119-27 - PubMed
  43. Clin Cancer Res. 2007 Sep 1;13(17):5001-9 - PubMed
  44. BMC Bioinformatics. 2007 Oct 18;8:403 - PubMed
  45. Bioinformatics. 2003;19 Suppl 1:i255-63 - PubMed
  46. Nat Biotechnol. 2011 Jul 31;29(8):742-9 - PubMed
  47. Clin Cancer Res. 2008 Oct 1;14(19):5959-66 - PubMed
  48. Nature. 2008 Nov 27;456(7221):470-6 - PubMed
  49. PLoS Comput Biol. 2013;9(7):e1003132 - PubMed
  50. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12837-42 - PubMed
  51. Bioinformatics. 2004 Jan 1;20(1):5-20 - PubMed
  52. Bioinformatics. 2007 Jul 15;23(14):1792-800 - PubMed
  53. Genes Immun. 2009 Jul;10(5):457-69 - PubMed
  54. Brief Funct Genomics. 2011 May;10(3):151-64 - PubMed
  55. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W239-45 - PubMed
  56. Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10146-51 - PubMed
  57. Annu Rev Biomed Eng. 2007;9:205-28 - PubMed
  58. Hum Mol Genet. 2002 Aug 15;11(17):1977-85 - PubMed
  59. BMC Bioinformatics. 2009 Mar 26;10:96 - PubMed
  60. Transpl Int. 2000;13 Suppl 1:S494-503 - PubMed
  61. Genome Biol. 2010;11(10):R106 - PubMed
  62. Science. 1995 Oct 20;270(5235):484-7 - PubMed
  63. Nucleic Acids Res. 2008 Dec;36(21):e141 - PubMed
  64. Bioinformatics. 2013 Mar 1;29(5):656-7 - PubMed
  65. Biometrics. 2009 Mar;65(1):40-51 - PubMed
  66. BMC Genomics. 2011 Mar 24;12:158 - PubMed
  67. Mol Endocrinol. 2012 Oct;26(10):1651-9 - PubMed
  68. BMC Bioinformatics. 2011 Aug 18;12:347 - PubMed
  69. Bioinformatics. 2010 Jan 1;26(1):139-40 - PubMed
  70. Biostatistics. 2013 Apr;14(2):232-43 - PubMed
  71. BMC Bioinformatics. 2010 Feb 03;11:72 - PubMed
  72. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9121-6 - PubMed
  73. J Neurosci. 2011 May 11;31(19):6939-43 - PubMed
  74. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 - PubMed
  75. Chronobiol Int. 2012 Apr;29(3):227-51 - PubMed
  76. Biomed Res Int. 2013;2013:203681 - PubMed
  77. Bioinformatics. 2010 Jan 1;26(1):136-8 - PubMed
  78. BMC Bioinformatics. 2013 Mar 09;14:91 - PubMed
  79. Trends Genet. 2007 Jan;23(1):42-50 - PubMed
  80. BMC Bioinformatics. 2010 Aug 10;11:422 - PubMed
  81. Mol Biol Cell. 1998 Dec;9(12):3273-97 - PubMed
  82. Bioinformatics. 2011 Jan 1;27(1):78-86 - PubMed
  83. Physiol Genomics. 2001 Apr 02;5(3):147-60 - PubMed
  84. Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11758-63 - PubMed
  85. Mol Syst Biol. 2010 Oct 5;6:419 - PubMed
  86. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2907-12 - PubMed
  87. Nature. 2011 Mar 24;471(7339):473-9 - PubMed
  88. Cell. 2011 Mar 18;144(6):874-85 - PubMed
  89. Exp Ther Med. 2011 Jul;2(4):705-713 - PubMed
  90. BMC Bioinformatics. 2005 Jun 29;6:165 - PubMed
  91. Adv Exp Med Biol. 2010;680:139-47 - PubMed
  92. Genome Biol. 2013;14(9):R95 - PubMed
  93. BMC Res Notes. 2013 Oct 24;6:428 - PubMed
  94. BMC Bioinformatics. 2006 Apr 05;7:191 - PubMed
  95. BMC Syst Biol. 2012 Jun 15;6:69 - PubMed
  96. Int Rev Neurobiol. 2004;60:25-58 - PubMed
  97. BMC Bioinformatics. 2008 Jun 18;9:287 - PubMed
  98. Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10903-8 - PubMed
  99. BMC Bioinformatics. 2007 May 01;8:142 - PubMed
  100. Nihon Rinsho. 2012 Jul;70(7):1109-14 - PubMed
  101. BMC Bioinformatics. 2010 Nov 16;11:564 - PubMed
  102. Biostatistics. 2012 Jul;13(3):523-38 - PubMed
  103. Stat Methods Med Res. 2013 Oct;22(5):519-36 - PubMed
  104. Nat Rev Genet. 2012 Sep;13(9):599 - PubMed
  105. Br J Surg. 2011 Sep;98(9):1309-17 - PubMed
  106. Stat Appl Genet Mol Biol. 2004;3:Article3 - PubMed
  107. PLoS Genet. 2007 Jun;3(6):e109 - PubMed
  108. BMC Biol. 2010 May 11;8:58 - PubMed
  109. Bioinformatics. 2003 Mar 1;19(4):474-82 - PubMed
  110. Bioinformatics. 2003 Aug 12;19(12):1477-83 - PubMed
  111. Nat Rev Genet. 2014 Jan;15(1):3 - PubMed
  112. Bioinformatics. 2011 Jul 1;27(13):i392-400 - PubMed
  113. Curr Opin Genet Dev. 2011 Aug;21(4):388-94 - PubMed
  114. Biometrics. 2005 Mar;61(1):10-6 - PubMed
  115. Bioinformatics. 2012 Aug 1;28(15):2004-7 - PubMed
  116. BMJ. 2002 Sep 28;325(7366):687 - PubMed

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