메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX; BIOLOGICAL ANALYTES; GENE STRUCTURE; GENE STRUCTURE PREDICTION; ISOFORMS; MICROARRAY EXPERIMENTS; REAL DATA SETS;

EID: 78649331051     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-578     Document Type: Article
Times cited : (3)

References (30)
  • 1
    • 67849087126 scopus 로고    scopus 로고
    • Alternative splicing in lung cancer
    • 10.1097/JTO.0b013e3181a520dc, 19461400
    • Pio R, Montuenga L. Alternative splicing in lung cancer. J Thorac Oncol 2009, 4(6):674-8. 10.1097/JTO.0b013e3181a520dc, 19461400.
    • (2009) J Thorac Oncol , vol.4 , Issue.6 , pp. 674-678
    • Pio, R.1    Montuenga, L.2
  • 2
    • 56749164864 scopus 로고    scopus 로고
    • Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
    • 10.1038/ng.264, 18978788
    • Castle J, Zhang C, Shah J, Kulkarni A, Kalsotra A, Cooper T, Johnson J. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 2008, 40(12):1416-25. 10.1038/ng.264, 18978788.
    • (2008) Nat Genet , vol.40 , Issue.12 , pp. 1416-1425
    • Castle, J.1    Zhang, C.2    Shah, J.3    Kulkarni, A.4    Kalsotra, A.5    Cooper, T.6    Johnson, J.7
  • 3
    • 34250756005 scopus 로고    scopus 로고
    • Probe selection and expression index computation of Affymetrix Exon Arrays
    • 10.1371/journal.pone.0000088, 1762343, 17183719
    • Xing Y, Kapur K, Wong W. Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE 2006, 1:e88. 10.1371/journal.pone.0000088, 1762343, 17183719.
    • (2006) PLoS ONE , vol.1
    • Xing, Y.1    Kapur, K.2    Wong, W.3
  • 4
    • 34547632484 scopus 로고    scopus 로고
    • Discovery of tissue-specific exons using comprehensive human exon microarrays
    • 10.1186/gb-2007-8-4-r64, 1896007, 17456239
    • Clark T, Schweitzer A, Chen T, Staples M, Lu G, Wang H, Williams A, Blume J. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol 2007, 8(4):R64. 10.1186/gb-2007-8-4-r64, 1896007, 17456239.
    • (2007) Genome Biol , vol.8 , Issue.4
    • Clark, T.1    Schweitzer, A.2    Chen, T.3    Staples, M.4    Lu, G.5    Wang, H.6    Williams, A.7    Blume, J.8
  • 5
    • 48249128721 scopus 로고    scopus 로고
    • FIRMA: a method for detection of alternative splicing from exon array data
    • 10.1093/bioinformatics/btn284, 2638867, 18573797
    • Purdom E, Simpson K, Robinson M, Conboy J, Lapuk A, Speed T. FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 2008, 24(15):1707-14. 10.1093/bioinformatics/btn284, 2638867, 18573797.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1707-1714
    • Purdom, E.1    Simpson, K.2    Robinson, M.3    Conboy, J.4    Lapuk, A.5    Speed, T.6
  • 6
    • 29144480020 scopus 로고    scopus 로고
    • ANOSVA: a statistical method for detecting splice variation from expression data
    • 10.1093/bioinformatics/bti1010, 15961447
    • Cline M, Blume J, Cawley S, Clark T, Hu J, Lu G, Salomonis N, Wang H, Williams A. ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics 2005, 21(Suppl 1):i107-15. 10.1093/bioinformatics/bti1010, 15961447.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Cline, M.1    Blume, J.2    Cawley, S.3    Clark, T.4    Hu, J.5    Lu, G.6    Salomonis, N.7    Wang, H.8    Williams, A.9
  • 7
    • 75249101203 scopus 로고    scopus 로고
    • ARH: predicting splice variants from genome-wide data with modified entropy
    • 10.1093/bioinformatics/btp626, 19889797
    • Rasche A, Herwig R. ARH: predicting splice variants from genome-wide data with modified entropy. Bioinformatics 2010, 26:84-90. 10.1093/bioinformatics/btp626, 19889797.
    • (2010) Bioinformatics , vol.26 , pp. 84-90
    • Rasche, A.1    Herwig, R.2
  • 8
    • 77953249890 scopus 로고    scopus 로고
    • Splicing factor and exon profiling across human tissues
    • 10.1093/nar/gkq008, 2875023, 20110256
    • de la Grange P, Gratadou L, Delord M, Dutertre M, Auboeuf D. Splicing factor and exon profiling across human tissues. Nucleic Acids Res 2010, 38(9):2825-38. 10.1093/nar/gkq008, 2875023, 20110256.
    • (2010) Nucleic Acids Res , vol.38 , Issue.9 , pp. 2825-2838
    • de la Grange, P.1    Gratadou, L.2    Delord, M.3    Dutertre, M.4    Auboeuf, D.5
  • 9
    • 0037012922 scopus 로고    scopus 로고
    • Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays
    • 10.1126/science.1069415, 11988574
    • Clark T, Sugnet C, Ares MJ. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 2002, 296(5569):907-10. 10.1126/science.1069415, 11988574.
    • (2002) Science , vol.296 , Issue.5569 , pp. 907-910
    • Clark, T.1    Sugnet, C.2    Ares, M.J.3
  • 11
    • 84886765612 scopus 로고    scopus 로고
    • Affymetrix
    • Affymetrix. , http://www.affymetrix.com
  • 12
    • 80053321355 scopus 로고    scopus 로고
    • Brainarray
    • Brainarray. , http://brainarray.mbni.med.umich.edu
  • 14
    • 75649121097 scopus 로고    scopus 로고
    • MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays
    • 10.1093/nar/gkp853, 2800219, 19854940
    • Turro E, Lewin A, Rose A, Dallman MJ, Richardson S. MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays. Nucl Acids Res 2010, 38:e4. 10.1093/nar/gkp853, 2800219, 19854940.
    • (2010) Nucl Acids Res , vol.38
    • Turro, E.1    Lewin, A.2    Rose, A.3    Dallman, M.J.4    Richardson, S.5
  • 15
    • 70349751764 scopus 로고    scopus 로고
    • Resolving deconvolution ambiguity in gene alternative splicing
    • 10.1186/1471-2105-10-237, 2739860, 19653895
    • She Y, Hubbell E, Wang H. Resolving deconvolution ambiguity in gene alternative splicing. BMC Bioinformatics 2009, 10:237. 10.1186/1471-2105-10-237, 2739860, 19653895.
    • (2009) BMC Bioinformatics , vol.10 , pp. 237
    • She, Y.1    Hubbell, E.2    Wang, H.3
  • 16
    • 75949093653 scopus 로고    scopus 로고
    • Identifiability of isoform deconvolution from junction arrays and RNA-Seq
    • 10.1093/bioinformatics/btp544, 19762346
    • Hiller D, Jiang H, Xu W, Wong W. Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics 2009, 25(23):3056-9. 10.1093/bioinformatics/btp544, 19762346.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3056-3059
    • Hiller, D.1    Jiang, H.2    Xu, W.3    Wong, W.4
  • 18
    • 71549165598 scopus 로고    scopus 로고
    • Bi-cross-validation of the SVD and the non-negative matrix factorization
    • Owen A, Perry P. Bi-cross-validation of the SVD and the non-negative matrix factorization. Annals of Applied Statistics 2009, 3(2):564-594.
    • (2009) Annals of Applied Statistics , vol.3 , Issue.2 , pp. 564-594
    • Owen, A.1    Perry, P.2
  • 19
    • 84870532154 scopus 로고    scopus 로고
    • GEO (Gene Expression Omnibus)
    • GEO (Gene Expression Omnibus). , http://www.ncbi.nlm.nih.gov/geo/
  • 20
    • 34250795169 scopus 로고    scopus 로고
    • Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays
    • 10.1158/0008-5472.CAN-06-2869, 17575129
    • French P, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent M, Luider T, Kros J, van der Spek P, Sillevis Smitt P. Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Res 2007, 67(12):5635-42. 10.1158/0008-5472.CAN-06-2869, 17575129.
    • (2007) Cancer Res , vol.67 , Issue.12 , pp. 5635-5642
    • French, P.1    Peeters, J.2    Horsman, S.3    Duijm, E.4    Siccama, I.5    van den Bent, M.6    Luider, T.7    Kros, J.8    van der Spek, P.9    Sillevis Smitt, P.10
  • 22
    • 48149096726 scopus 로고    scopus 로고
    • MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays
    • 10.1261/rna.1070208, 2491471, 18566192
    • Xing Y, Stoilov P, Kapur K, Han A, Jiang H, Shen S, Black D, Wong W. MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 2008, 14(8):1470-9. 10.1261/rna.1070208, 2491471, 18566192.
    • (2008) RNA , vol.14 , Issue.8 , pp. 1470-1479
    • Xing, Y.1    Stoilov, P.2    Kapur, K.3    Han, A.4    Jiang, H.5    Shen, S.6    Black, D.7    Wong, W.8
  • 23
    • 38649129366 scopus 로고    scopus 로고
    • Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis
    • 10.1261/rna.725208, 2212255, 18073345
    • Hung L, Heiner M, Hui J, Schreiner S, Benes V, Bindereif A. Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis. RNA 2008, 14(2):284-96. 10.1261/rna.725208, 2212255, 18073345.
    • (2008) RNA , vol.14 , Issue.2 , pp. 284-296
    • Hung, L.1    Heiner, M.2    Hui, J.3    Schreiner, S.4    Benes, V.5    Bindereif, A.6
  • 24
    • 57249116888 scopus 로고    scopus 로고
    • Cross-hybridization modeling on Affymetrix exon arrays
    • 10.1093/bioinformatics/btn571, 2639301, 18984598
    • Kapur K, Jiang H, Xing Y, Wong W. Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics 2008, 24(24):2887-93. 10.1093/bioinformatics/btn571, 2639301, 18984598.
    • (2008) Bioinformatics , vol.24 , Issue.24 , pp. 2887-2893
    • Kapur, K.1    Jiang, H.2    Xing, Y.3    Wong, W.4
  • 25
    • 61449107655 scopus 로고    scopus 로고
    • Microarray background correction: maximum likelihood estimation for the normal-exponential convolution
    • 10.1093/biostatistics/kxn042, 2648902, 19068485
    • Silver J, Ritchie M, Smyth G. Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics 2009, 10(2):352-63. 10.1093/biostatistics/kxn042, 2648902, 19068485.
    • (2009) Biostatistics , vol.10 , Issue.2 , pp. 352-363
    • Silver, J.1    Ritchie, M.2    Smyth, G.3
  • 26
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249, 12925520
    • Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U, Speed T. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-64. 10.1093/biostatistics/4.2.249, 12925520.
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.4    Antonellis, K.5    Scherf, U.6    Speed, T.7
  • 27
    • 84888281484 scopus 로고    scopus 로고
    • Aroma.affymetrix
    • Aroma.affymetrix. , http://www.aroma-project.org/
  • 30
    • 62349102835 scopus 로고    scopus 로고
    • GenomeGraphs: integrated genomic data visualization with R
    • 10.1186/1471-2105-10-2, 2629762, 19123956
    • Durinck S, Bullard J, Spellman P, Dudoit S. GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics 2009, 10:2. 10.1186/1471-2105-10-2, 2629762, 19123956.
    • (2009) BMC Bioinformatics , vol.10 , pp. 2
    • Durinck, S.1    Bullard, J.2    Spellman, P.3    Dudoit, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.