References

  1. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes.

    Nature 2008 , 456:470-476. PubMed Abstract | Publisher Full Text OpenURL

  2. Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavare S, Ritchie ME: Statistical issues in the analysis of Illumina data.

    BMC Bioinformatics 2008 , 9:85. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  3. Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays.

    J Comput Biol 2005 , 12:882-893. PubMed Abstract | Publisher Full Text OpenURL

  4. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al.: A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

    Science 2008 , 321:956-960. PubMed Abstract | Publisher Full Text OpenURL

  5. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al.: Stem cell transcriptome profiling via massive-scale mRNA sequencing.

    Nat Methods 2008 , 5:613-619. PubMed Abstract | Publisher Full Text OpenURL

  6. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y: RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays.

    Genome Res 2008 , 18:1509-1517. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  7. Huang da W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

    Nat Protoc 2009 , 4:44-57. PubMed Abstract | Publisher Full Text OpenURL

  8. Huang da W, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

    Nucleic Acids Res 2009 , 37:1-13. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  9. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

    Biostatistics 2003 , 4:249-264. PubMed Abstract | Publisher Full Text OpenURL

  10. Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments.

    Stat Appl Genet Mol Biol 2004 , 3:Article3. PubMed Abstract | Publisher Full Text OpenURL

  11. Audic S, Claverie JM: The significance of digital gene expression profiles.

    Genome Res 1997 , 7:986-995. PubMed Abstract | Publisher Full Text OpenURL