Shah SH, Pallas JA: Identifying differential exon splicing using linear models and correlation coefficients. BMC Bioinformatics. 2009, 10: 26-10.1186/1471-2105-10-26.
Article
PubMed Central
PubMed
Google Scholar
Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y: Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet. 2008, 4 (10): e1000225-10.1371/journal.pgen.1000225.
Article
PubMed Central
PubMed
Google Scholar
Sugnet CW, Srinivasan K, Clark TA, O’Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D: Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol. 2006, 2 (1): e4-10.1371/journal.pcbi.0020004.
Article
PubMed Central
PubMed
Google Scholar
Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y: Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A. 2011, 108 (7): 2837-2842. 10.1073/pnas.1012834108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Affymetrix website.http://www.affymetrix.com/estore/browse/products.jsp?productId=131452#1_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. Nat. 2008, 456 (7221): 470-476. 10.1038/nature07509.
Article
CAS
Google Scholar
Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ: Alternative expression analysis by RNA sequencing. Nat Methods. 2010, 7 (10): 843-847. 10.1038/nmeth.1503.
Article
CAS
PubMed
Google Scholar
Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, Rye IH, Nyberg S, Wolf M, Borresen-Dale AL: Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol. 2011, 12 (1): R6-10.1186/gb-2011-12-1-r6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S: Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics. 2011, 4: 11-10.1186/1755-8794-4-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK: Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nat. 2010, 464 (7289): 768-772. 10.1038/nature08872.
Article
CAS
Google Scholar
Richard H, Schulz MH, Sultan M, Nurnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M: Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res. 2010, 38 (10): e112-10.1093/nar/gkq041.
Article
PubMed Central
PubMed
Google Scholar
Deininger PL, Batzer MA: Alu repeats and human disease. Mol Genet Metab. 1999, 67 (3): 183-193. 10.1006/mgme.1999.2864.
Article
CAS
PubMed
Google Scholar
Hsieh SY, Chen WY, Yeh TS, Sheen IS, Huang SF: High-frequency Alu-mediated genomic recombination/deletion within the caspase-activated DNase gene in human hepatoma. Oncogene. 2005, 24 (43): 6584-6589.
CAS
PubMed
Google Scholar
Belancio VP, Roy-Engel AM, Deininger PL: All y’all need to know ’bout retroelements in cancer. Semin Cancer Biol. 2010, 20 (4): 200-210. 10.1016/j.semcancer.2010.06.001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang W, Edwards A, Fan W, Deininger P, Zhang K: Alu distribution and mutation types of cancer genes. BMC Genomics. 2011, 12: 157-10.1186/1471-2164-12-157.
Article
PubMed Central
CAS
PubMed
Google Scholar
Testori A, Caizzi L, Cutrupi S, Friard O, De Bortoli M, Cora D, Caselle M: The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors. BMC Genomics. 2012, 13: 400-10.1186/1471-2164-13-400.
Article
PubMed Central
CAS
PubMed
Google Scholar
Singer SS, Mannel DN, Hehlgans T, Brosius J, Schmitz J: From “junk” to gene: curriculum vitae of a primate receptor isoform gene. J Mol Biol. 2004, 341 (4): 883-886. 10.1016/j.jmb.2004.06.070.
Article
CAS
PubMed
Google Scholar
Krull M, Brosius J, Schmitz J: Alu-SINE exonization: en route to protein-coding function. Mol Biol Evol. 2005, 22 (8): 1702-1711. 10.1093/molbev/msi164.
Article
CAS
PubMed
Google Scholar
Sorek R: The birth of new exons: mechanisms and evolutionary consequences. RNA. 2007, 13 (10): 1603-1608. 10.1261/rna.682507.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sela N, Mersch B, Hotz-Wagenblatt A, Ast G: Characteristics of transposable element exonization within human and mouse. PLoS One. 2010, 5 (6): e10907-10.1371/journal.pone.0010907.
Article
PubMed Central
PubMed
Google Scholar
Levy A, Sela N, Ast G: TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res. 2008, 36 (Database issue): D47-D52.
PubMed Central
CAS
PubMed
Google Scholar
Sorek R, Ast G, Graur D: Alu-containing exons are alternatively spliced. Genome Res. 2002, 12 (7): 1060-1067. 10.1101/gr.229302.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G: Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu’s unique role in shaping the human transcriptome. Genome Biol. 2007, 8 (6): R127-10.1186/gb-2007-8-6-r127.
Article
PubMed Central
PubMed
Google Scholar
Hasler J, Strub K: Alu elements as regulators of gene expression. Nucleic Acids Res. 2006, 34 (19): 5491-5497. 10.1093/nar/gkl706.
Article
PubMed Central
PubMed
Google Scholar
Hasler J, Strub K: Alu RNP and Alu RNA regulate translation initiation in vitro. Nucleic Acids Res. 2006, 34 (8): 2374-2385. 10.1093/nar/gkl246.
Article
PubMed Central
PubMed
Google Scholar
Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ: Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics. 2009, 10: 563-10.1186/1471-2164-10-563.
Article
PubMed Central
PubMed
Google Scholar
Ponicsan SL, Kugel JF, Goodrich JA: Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev. 2010, 20 (2): 149-155. 10.1016/j.gde.2010.01.004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vorechovsky I: Transposable elements in disease-associated cryptic exons. Hum Genet. 2010, 127 (2): 135-154. 10.1007/s00439-009-0752-4.
Article
CAS
PubMed
Google Scholar
Mitchell GA, Labuda D, Fontaine G, Saudubray JM, Bonnefont JP, Lyonnet S, Brody LC, Steel G, Obie C, Valle D: Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation. Proc Natl Acad Sci U S A. 1991, 88 (3): 815-819. 10.1073/pnas.88.3.815.
Article
PubMed Central
CAS
PubMed
Google Scholar
Amit M, Sela N, Keren H, Melamed Z, Muler I, Shomron N, Izraeli S, Ast G: Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC Mol Biol. 2007, 8: 109-10.1186/1471-2199-8-109.
Article
PubMed Central
PubMed
Google Scholar
Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G: Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol. 2009, 5 (3): e1000300-10.1371/journal.pcbi.1000300.
Article
PubMed Central
PubMed
Google Scholar
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y: Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 2010, 20 (2): 180-189. 10.1101/gr.099226.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M: Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res. 2011, 21 (7): 1028-1041. 10.1101/gr.119347.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET: Transcriptome genetics using second generation sequencing in a Caucasian population. Nat. 2010, 464 (7289): 773-777. 10.1038/nature08903.
Article
CAS
Google Scholar
Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L: Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One. 2011, 6 (2): e17490-10.1371/journal.pone.0017490.
Article
PubMed Central
CAS
PubMed
Google Scholar
SRA website.http://www.ncbi.nlm.nih.gov/sra,
UCSC Genome Brower website.http://genome.ucsc.edu/,
Huang W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009, 4 (1): 44-57.
Article
CAS
Google Scholar
Emerson RO, Thomas JH: Adaptive evolution in zinc finger transcription factors. PLoS Genet. 2009, 5 (1): e1000325-10.1371/journal.pgen.1000325.
Article
PubMed Central
PubMed
Google Scholar
Giordano J, Ge Y, Gelfand Y, Abrusan G, Benson G, Warburton PE: Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol. 2007, 3 (7): e137-10.1371/journal.pcbi.0030137.
Article
PubMed Central
PubMed
Google Scholar
Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB: Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 2008, 18 (12): 1865-1874. 10.1101/gr.081422.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jurka J: Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci U S A. 1997, 94 (5): 1872-1877. 10.1073/pnas.94.5.1872.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang K, Fan W, Deininger P, Edwards A, Xu Z, Zhu D: Breaking the computational barrier: a divide-conquer and aggregate based approach for Alu insertion site characterisation. Int J Comput Biol Drug Des. 2009, 2 (4): 302-322. 10.1504/IJCBDD.2009.030763.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dogan RI, Getoor L, Wilbur WJ, Mount SM: SplicePort--an interactive splice-site analysis tool. Nucleic Acids Res. 2007, 35 (Web Server issue): W285-W291.
Article
PubMed Central
PubMed
Google Scholar
Fullwood MJ, Wei CL, Liu ET, Ruan Y: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009, 19 (4): 521-532. 10.1101/gr.074906.107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25 (9): 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pertea M, Lin X, Salzberg SL: GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res. 2001, 29 (5): 1185-1190. 10.1093/nar/29.5.1185.
Article
PubMed Central
CAS
PubMed
Google Scholar
DAVID website.http://david.abcc.ncifcrf.gov/,
Tophat website.http://tophat.cbcb.umd.edu/,
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.
Article
CAS
PubMed
Google Scholar
Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P: SMART 4.0: towards genomic data integration. Nucleic Acids Res. 2004, 32 (Database issue): D142-D144.
Article
PubMed Central
CAS
PubMed
Google Scholar