Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Chen, Geng ^a   Li, Ruiyuan ^b   Shi, Leming ^c   Qi, Junyi ^a   Hu, Pengzhan ^a   Luo, Jian ^a   Liu, Mingyao ^a   Shi, Tieliu ^a,d  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^d Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; RNA;

AFRICAN; AMINO ACID SEQUENCE; ARTICLE; ASIAN; BRAIN CELL; CAUCASIAN; CELL LINE; CONTIG MAPPING; ETHNICITY; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE DELETION; GENE EXPRESSION; HUMAN; HUMAN GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ASSEMBLY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ALIGNMENT; SPLICEOSOME; BRAIN; GENETICS; GENOME; METABOLISM; POLYMERASE CHAIN REACTION; VALIDATION STUDY;

PAN;

BRAIN; CELL LINE; GENE EXPRESSION; GENOME; HUMANS; POLYMERASE CHAIN REACTION; RNA;

EID: 82455162834     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-590     Document Type: Article

References (34)

1. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, et al. Large-scale copy number polymorphism in the human genome. Science 2004, 305(5683):525-528. 10.1126/science.1098918, 15273396.
2. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, et al. Fine-scale structural variation of the human genome. Nat Genet 2005, 37(7):727-732. 10.1038/ng1562, 15895083.
3. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature 2006, 444(7118):444-454. 10.1038/nature05329, 2669898, 17122850.
4. Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 2006, 38(1):82-85. 10.1038/ng1695, 16327809.
5. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, et al. Common deletion polymorphisms in the human genome. Nat Genet 2006, 38(1):86-92. 10.1038/ng1696, 16468122.
6. Wu X, Xiao H. Progress in the detection of human genome structural variations. Sci China C Life Sci 2009, 52(6):560-567. 10.1007/s11427-009-0078-4, 19557334.
7. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316(5830):1484-1488. 10.1126/science.1138341, 17510325.
8. Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 2007, 8(6):413-423.
9. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346.
10. 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(5891):956-960. 10.1126/science.1160342, 18599741.
11. Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, et al. Genome assembly comparison identifies structural variants in the human genome. Nat Genet 2006, 38(12):1413-1418. 10.1038/ng1921, 2674632, 17115057.
12. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, et al. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods 2010, 7(5):365-371. 10.1038/nmeth.1451, 2875995, 20440878.
13. Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J, et al. Building the sequence map of the human pan-genome. Nat Biotechnol 2010, 28(1):57-63. 10.1038/nbt.1596, 19997067.
14. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453(7199):1239-1243. 10.1038/nature07002, 18488015.
15. 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(9):1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
16. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10(1):57-63. 10.1038/nrg2484, 2949280, 19015660.
17. Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive transcriptome analysis. Curr Protoc Mol Biol 2010, (Chapter 4):11-13. Unit 4 11.
18. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28(8):827-838. 10.1038/nbt.1665, 20676074.
19. Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, et al. Universal Reference RNA as a standard for microarray experiments. BMC Genomics 2004, 5(1):20. 10.1186/1471-2164-5-20, 394318, 15113400.
20. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
21. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19(Suppl 2):ii215-225. 10.1093/bioinformatics/btg1080, 14534192.
22. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
23. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
24. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515. 10.1038/nbt.1621, 3146043, 20436464.
25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
26. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386.
27. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al. The diploid genome sequence of an individual human. PLoS Biol 2007, 5(10):e254. 10.1371/journal.pbio.0050254, 1964779, 17803354.
28. Holland KA, Richardson N, Somasekaram A, Navaratnam N. RNA editing. Front Horm Res 1999, 25:101-121.
29. Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods 2009, 6(11 Suppl):S6-S12.
30. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
31. Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011, 12(2):87-98. 10.1038/nrg2934, 3031867, 21191423.
32. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008, 18(5):810-820. 10.1101/gr.7337908, 2336810, 18340039.
33. Teng X, Xiao H. Perspectives of DNA microarray and next-generation DNA sequencing technologies. Sci China C Life Sci 2009, 52(1):7-16. 10.1007/s11427-009-0012-9, 19152079.
34. Li Y, Wang J. Faster human genome sequencing. Nat Biotechnol 2009, 27(9):820-821. 10.1038/nbt0909-820, 19741637.