Observations on novel splice junctions from RNA sequencing data

Biochemical and Biophysical Research Communications

Volumn 409, Issue 2, 2011, Pages 299-303

  Wang, Likun ^a,b   Wang, Xiaowo ^b   Wang, Xi ^b   Liang, Yanchun ^a   Zhang, Xuegong ^b  

^a JILIN UNIVERSITY   (China)

^b TSINGHUA UNIVERSITY   (China)

Author keywords

Alternative splicing; Differential expression; RNA sequencing; Sequencing depth; Splice junction detection

Indexed keywords

RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CANONICAL ANALYSIS; CONTROLLED STUDY; HUMAN; HUMAN CELL; OBSERVATION; PRIORITY JOURNAL; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY;

ALTERNATIVE SPLICING; CELLS, CULTURED; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RNA SPLICING; SEQUENCE ANALYSIS, RNA;

EID: 79957894499     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2011.05.005     Document Type: Article

References (27)

1. Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 40:1413-1415.
2. Wang G.S., Cooper T.A. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat. Rev. Genet. 2007, 8:749-761.
3. Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., Burge C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
4. Adams M.D., Soares M.B., Kerlavage A.R., Fields C., Venter J.C. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat. Genet. 1993, 4:373-380.
5. Johnson J.M., Castle J., Garrett-Engele P., Kan Z., Loerch P.M., Armour C.D., Santos R., Schadt E.E., Stoughton R., Shoemaker D.D. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302:2141-2144.
6. Ule J., Ule A., Spencer J., Williams A., Hu J.S., Cline M., Wang H., Clark T., Fraser C., Ruggiu M., Zeeberg B.R., Kane D., Weinstein J.N., Blume J., Darnell R.B. Nova regulates brain-specific splicing to shape the synapse. Nat. Genet. 2005, 37:844-852.
7. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
8. Au K.F., Jiang H., Lin L., Xing Y., Wong W.H. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 2010, 38:4570-4578.
9. Wang K., Singh D., Zeng Z., Coleman S.J., Huang Y., Savich G.L., He X., Mieczkowski P., Grimm S.A., Perou C.M., MacLeod J.N., Chiang D.Y., Prins J.F., Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010, 38:e178.
10. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
11. Filichkin S.A., Priest H.D., Givan S.A., Shen R., Bryant D.W., Fox S.E., Wong W.K., Mockler T.C. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 2010, 20:45-58.
12. Burset M., Seledtsov I.A., Solovyev V.V. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res. 2000, 28:4364-4375.
13. E. Birney, J.A. Stamatoyannopoulos, A. Dutta, R. Guigo, T.R. Gingeras, E.H. Margulies, Z.P. Weng, M. Snyder, E.T. Dermitzakis, J.A. Stamatoyannopoulos, R.E. Thurman, M.S. Kuehn, C.M. Taylor, S. Neph, C.M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J.A. Greenbaum, R.M. Andrews, P. Flicek, P.J. Boyle, H. Cao, N.P. Carter, G.K. Clelland, S. Davis, N. Day, P. Dhami, S.C. Dillon, M.O. Dorschner, H. Fiegler, P.G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K.D. James, B.E. Johnson, E.M. Johnson, T.T. Frum, E.R. Rosenzweig, N. Karnani, K. Lee, G.C. Lefebvre, P.A. Navas, F. Neri, S.C.J. Parker, P.J. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F.S. Collins, J. Dekker, J.D. Lieb, T.D. Tullius, G.E. Crawford, S. Sunyaev, W.S. Noble, I. Dunham, A. Dutta, R. Guigo, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D.Y. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. Sandelin, I.L. Hofacker, R. Baertsch, D. Keefe, P. Flicek, S. Dike, J. Cheng, H.A. Hirsch, E.A. Sekinger, J. Lagarde, J.F. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermuller, J. Hertel, M. Lindemeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J.S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews et al., Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 447 (2007) pp. 799-816.
14. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
15. Pruitt K.D., Tatusova T., Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35:D61-65.
16. Curwen V., Eyras E., Andrews T.D., Clarke L., Mongin E., Searle S.M., Clamp M. The Ensembl automatic gene annotation system. Genome Res. 2004, 14:942-950.
17. Hsu F., Kent W.J., Clawson H., Kuhn R.M., Diekhans M., Haussler D. The UCSC Known Genes. Bioinformatics 2006, 22:1036-1046.
18. Harrow J., Denoeud F., Frankish A., Reymond A., Chen C.K., Chrast J., Lagarde J., Gilbert J.G., Storey R., Swarbreck D., Rossier C., Ucla C., Hubbard T., Antonarakis S.E., Guigo R. GENCODE: producing a reference annotation for ENCODE. Genome Biology 2006, 7(Suppl. 1):S4 1-9.
19. Boguski M.S., Lowe T.M., Tolstoshev C.M. dbEST - database for "expressed sequence tags" Nat. Genet. 1993, 4:332-333.
20. van Bakel H., Nislow C., Blencowe B.J., Hughes T.R. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 2010, 8:e1000371.
21. Wang L., Feng Z., Wang X., Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010, 26:136-138.
22. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., Speed T.P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30:e15.
23. Wang D., Bodovitz S. Single cell analysis: the new frontier in 'omics'. Trends Biotechnol. 2010, 28:281-290.
24. Lipson D., Raz T., Kieu A., Jones D.R., Giladi E., Thayer E., Thompson J.F., Letovsky S., Milos P., Causey M. Quantification of the yeast transcriptome by single-molecule sequencing. Nat. Biotechnol. 2009, 27:652-658.
25. Harris T.D., Buzby P.R., Babcock H., Beer E., Bowers J., Braslavsky I., Causey M., Colonell J., Dimeo J., Efcavitch J.W., Giladi E., Gill J., Healy J., Jarosz M., Lapen D., Moulton K., Quake S.R., Steinmann K., Thayer E., Tyurina A., Ward R., Weiss H., Xie Z. Single-molecule DNA sequencing of a viral genome. Science 2008, 320:106-109.
26. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., Bibillo A., Bjornson K., Chaudhuri B., Christians F., Cicero R., Clark S., Dalal R., Dewinter A., Dixon J., Foquet M., Gaertner A., Hardenbol P., Heiner C., Hester K., Holden D., Kearns G., Kong X., Kuse R., Lacroix Y., Lin S., Lundquist P., Ma C., Marks P., Maxham M., Murphy D., Park I., Pham T., Phillips M., Roy J., Sebra R., Shen G., Sorenson J., Tomaney A., Travers K., Trulson M., Vieceli J., Wegener J., Wu D., Yang A., Zaccarin D., Zhao P., Zhong F., Korlach J., Turner S. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
27. Jiang H., Wong W.H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 2008, 24:2395-2396.