FDM: A graph-based statistical method to detect differential transcription using RNA-seq data

Bioinformatics

Volumn 27, Issue 19, 2011, Pages 2633-2640

  Singh, Darshan ^a   Orellana, Christian F ^a   Hu, Yin ^b   Jones, Corbin D ^c   Liu, Yufeng ^d   Chiang, Derek Y ^e   Liu, Jinze ^b   Prins, Jan F ^a  

^a Brooks Computer Science Building   (United States)

^b UNIVERSITY OF KENTUCKY   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d University of North Carolina at Chapel Hill   (United States)

^e UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

ISOPROTEIN; RNA; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ARTICLE; BIOLOGICAL MODEL; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; GENOME; HUMAN; METHODOLOGY; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; GENE EXPRESSION PROFILING; GENOME; HUMANS; MODELS, GENETIC; PROTEIN ISOFORMS; RNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 80053435328     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr458     Document Type: Article

References (17)

1. Bohnert, R. and Rätsch, G. (2010) rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res., 38 (Suppl. 2), W348-W351.
2. Guttman, M. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510.
3. Hansen, K.D. et al. (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res., 38, e131.
4. Heber, S. et al. (2002) Splicing graphs and EST assembly problem. Bioinformatics, 18 (Suppl. 1), S181-S188.
5. Hu, Y. et al. (2010) A probabilistic framework for aligning paired-end RNA-seq data. Bioinformatics, 26, 1950-1957.
6. Jean, G. et al. (2010) RNA-Seq Read Alignments with PALMapper. Current Protocols in Bioinformatics. Available at http://www.hpa.org.uk./infections/topics_az/antimicrobial_resistance/amr.pdf, pp. 32:11.6.1-32:11.6.37.
7. Kwan, T. et al. (2008) Genome-wide analysis of transcript isoform variation in humans. Nat. Genet., 40, 225-231.
8. Pan, Q. et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
9. Robertson, G. et al. (2010) De novo assembly and analysis of RNA-seq data. Nat. Methods, 7, 909-912.
10. Roberts, A. et al. (2011) Improving rna-seq expression estimates by correcting for fragment bias. Genome Biol., 12, R22.
11. Stegle, O. et al. (2010) Statistical tests for detecting differential rna-transcript expression from read counts. Nat. Preced. [Epub ahead of print, doi:10.1038/npre.2010.4437.1, May 11, 2010].
12. Sultan, M. et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956-960.
13. Trapnell, C. et al. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
14. Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
15. Wang, E.T. et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
16. Wang, Z. et al. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
17. Wang, K. et al. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, e178.