CLASS2: Accurate and efficient splice variant annotation from RNA-seq reads

Nucleic Acids Research

Volumn 44, Issue 10, 2016, Pages

  Song, Li ^a,b   Sabunciyan, Sarven ^a   Florea, Liliana ^a,b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Johns Hopkins University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; TRANSCRIPTOME; ISOPROTEIN; POLYADENYLIC ACID; RNA;

ACCURACY; ALTERNATIVE RNA SPLICING; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC MODEL; GENETIC VARIATION; GENOME ANALYSIS; PRIORITY JOURNAL; RELIABILITY; RNA SEQUENCE; RNA TRANSCRIPTION; SCORING SYSTEM; TRANSCRIPTOMICS; ALGORITHM; EXON; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INTRON; MOLECULAR GENETICS; PEACH; POLYMERASE CHAIN REACTION; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

ALGORITHMS; ALTERNATIVE SPLICING; EXONS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTRONS; MOLECULAR SEQUENCE ANNOTATION; POLY A; POLYMERASE CHAIN REACTION; PROTEIN ISOFORMS; PRUNUS PERSICA; REPRODUCIBILITY OF RESULTS; RNA; RNA, RIBOSOMAL; SOFTWARE;

EID: 84973462003     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw158     Document Type: Article

References (36)

1. Kelemen, O., Convertini, P., Zhang, Z., Wen, Y., Shen, M., Falaleeva, M., Stamm, S. (2012) Function of alternative splicing. Gene, 514, 1-30.
2. Tazi, J., Bakkour, N., Stamm, S. (2009) Alternative splicing and disease. Biochim. Biophys. Acta, 1792, 14-26.
3. Singh, R. K., Cooper, T. A. (2012) Pre-mRNA splicing in disease and therapeutics. Trends Mol. Med., 18, 472-482.
4. Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., Burge, C. B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476.
5. Pan, Q., Shai, O., Lee, L. J., Frey, B. J., Blencowe, B. J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
6. Fonseca, N. A., Rung, J., Brazma, A., Marioni, J. C. (2012) Tools for mapping high-throughput sequencing data. Bioinformatics, 28, 3169-3177.
7. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., Pachter, L. (2009) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
8. Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C. 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.
9. Li, W., Feng, J., Jiang, T. (2011) IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. J. Comput. Biol., 18, 1693-1707.
10. Mezlini, A. M., Smith, E. J., Fiume, M., Buske, O., Savich, G. L., Shah, S., Aparicio, S., Chiang, D. Y., Goldenberg, A., Brudno, M. (2013) iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res., 23, 519-529.
11. Li, J. J., Jiang, C. R., Brown, J. B., Huang, H., Bickel, P. J. (2011) Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc. Natl. Acad. Sci. U. S. A., 108, 19867-19872.
12. Florea, L. D., Salzberg, S. L. (2013) Genome-guided transcriptome assembly in the age of next-generation sequencing. IEEE/ACM Trans. Comput. Biol. Bioinform., 10, 1234-1240.
13. Rogers, M. F., Thomas, J., Reddy, A. S., Ben-Hur, A. (2012) SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol., 13, R4.
14. Florea, L., Di Francesco, V., Miller, J., Turner, R., Yao, A., Harris, M., Walenz, B., Mobarry, C., Merkulov, G. V., Charlab, R. et al. (2005) Gene and alternative splicing annotation with AIR. Genome Res., 15, 54-66.
15. Song, L., Florea, L. (2013) CLASS: constrained transcript assembly of RNA-seq reads. BMC Bioinformatics, 14(Suppl. 5), S14.
16. Ameur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L., Feuk, L. (2011) Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat. Struct. Mol. Biol., 18, 1435-1440.
17. Griebel, T., Zacher, B., Ribeca, P., Raineri, E., Lacroix, V., Guigo, R., Sammeth, M. (2012) Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res., 40, 10073-10083.
18. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S. L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
19. Florea, L., Song, L., Salzberg, S. L. (2013) Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Research, 2, 188.
20. Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
21. Sveen, A., Johannessen, B., Teixeira, M. R., Lothe, R. A., Skotheim, R. I. (2014) Transcriptome instability as a molecular pan-cancer characteristic of carcinomas. BMC Genomics, 15, 672.
22. Eswaran, J., Horvath, A., Godbole, S., Reddy, S., Mudvari, P., Ohshiro, K., Pakala, S. B., Cyanam, D., Nair, S. S., Fuqua, S. et al. (2013) RNA sequencing of cancer reveals novel splicing alterations. Sci. Rep., 3, 1689.
23. de Miguel, F. J., Sharma, R. D., Pajares, M. J., Montuenga, L. M., Rubio, A., Pio, R. (2014) Identification of alternative splicing events regulated by the oncogenic factor SRSF1 in lung cancer. Cancer Res., 74, 1105-1115.
24. Pimentel, H., Parra, M., Gee, S. L., Mohandas, N., Pachter, L., Conboy, J. G. (2015) A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res., 44, 838-851.
25. Jung, H., Lee, D., Lee, J., Park, D., Kim, Y. J., Park, W. Y., Hong, D., Park, P. J., Lee, E. (2015) Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat. Genet., 47, 1242-1248.
26. Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakraborty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., Guigo, R. (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res., 22, 1616-1625.
27. Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F. et al. (2012) Landscape of transcription in human cells. Nature, 489, 101-108.
28. Steijger, T., Abril, J. F., Engstrom, P. G., Kokocinski, F., Hubbard, T. J., Guigo, R., Harrow, J., Bertone, P., Consortium, R. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods, 10, 1177-1184.
29. Carrara, M., Lum, J., Cordero, F., Beccuti, M., Poidinger, M., Donatelli, S., Calogero, R. A., Zolezzi, F. (2015) Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinform., 16 (Suppl 9), S2.
30. Pickrell, J. K., Pai, A. A., Gilad, Y., Pritchard, J. K. (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet., 6, e1001236.
31. Elkon, R., Ugalde, A. P., Agami, R. (2013) Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet., 14, 496-506.
32. Di Giammartino, D. C., Nishida, K., Manley, J. L. (2011) Mechanisms and consequences of alternative polyadenylation. Mol. Cell, 43, 853-866.
33. Kang, Y. N., Lai, D. P., Ooi, H. S., Shen, T. T., Kou, Y., Tian, J., Czajkowsky, D. M., Shao, Z., Zhao, X. (2014) Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast. Mol. Genet. Genomics, 290, 217-224.
34. Derti, A., Garrett-Engele, P., Macisaac, K. D., Stevens, R. C., Sriram, S., Chen, R., Rohl, C. A., Johnson, J. M., Babak, T. (2012) A quantitative atlas of polyadenylation in five mammals. Genome Res., 22, 1173-1183.
35. Behr, J., Kahles, A., Zhong, Y., Sreedharan, V. T., Drewe, P., Ratsch, G. (2013) MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics, 29, 2529-2538.
36. Hormozdiari, F., Hajirasouliha, I., McPherson, A., Eichler, E. E., Sahinalp, S. C. (2011) Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Res., 21, 2203-2212.