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Volumn 14, Issue SUPPL.5, 2013, Pages

Gene set enrichment analysis of RNA-Seq data: Integrating differential expression and splicing

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SPLICING; BIOLOGICAL DISCOVERIES; DIFFERENTIAL EXPRESSIONS; FUNCTIONAL ANALYSIS METHOD; FUNCTIONAL ENRICHMENT ANALYSIS; GENE SET ENRICHMENT ANALYSIS; NEGATIVE BINOMIAL DISTRIBUTION; TRANSCRIPTOME PROFILING;

EID: 84876153678     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S5-S16     Document Type: Article
Times cited : (48)

References (45)
  • 1
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • 10.1038/nmeth.1226, 18516045
    • 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.
    • (2008) Nat Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 3
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • 10.1038/ng.259, 18978789
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40(12):1413-1415. 10.1038/ng.259, 18978789.
    • (2008) Nat Genet , vol.40 , Issue.12 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 4
  • 5
    • 80054771709 scopus 로고    scopus 로고
    • RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma
    • 10.1371/journal.pone.0026168, 3197143, 22043308
    • Huang Q, Lin B, Liu H, Ma X, Mo F, Yu W, Li L, Li H, Tian T, Wu D, et al. RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PLoS One 2011, 6(10):e26168. 10.1371/journal.pone.0026168, 3197143, 22043308.
    • (2011) PLoS One , vol.6 , Issue.10
    • Huang, Q.1    Lin, B.2    Liu, H.3    Ma, X.4    Mo, F.5    Yu, W.6    Li, L.7    Li, H.8    Tian, T.9    Wu, D.10
  • 6
    • 84862777104 scopus 로고    scopus 로고
    • RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings
    • 10.1038/cr.2012.30, 22349460
    • Ren S, Peng Z, Mao JH, Yu Y, Yin C, Gao X, Cui Z, Zhang J, Yi K, Xu W, et al. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res 2012, 22(5):806-821. 10.1038/cr.2012.30, 22349460.
    • (2012) Cell Res , vol.22 , Issue.5 , pp. 806-821
    • Ren, S.1    Peng, Z.2    Mao, J.H.3    Yu, Y.4    Yin, C.5    Gao, X.6    Cui, Z.7    Zhang, J.8    Yi, K.9    Xu, W.10
  • 8
    • 84860430130 scopus 로고    scopus 로고
    • Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia
    • 10.1371/journal.pone.0036351, 3338678, 22558445
    • Wu JQ, Wang X, Beveridge NJ, Tooney PA, Scott RJ, Carr VJ, Cairns MJ. Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia. PLoS One 2012, 7(4):e36351. 10.1371/journal.pone.0036351, 3338678, 22558445.
    • (2012) PLoS One , vol.7 , Issue.4
    • Wu, J.Q.1    Wang, X.2    Beveridge, N.J.3    Tooney, P.A.4    Scott, R.J.5    Carr, V.J.6    Cairns, M.J.7
  • 9
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    • 10.1093/bioinformatics/btp612, 19855105
    • Wang L, Feng Z, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010, 26(1):136-138. 10.1093/bioinformatics/btp612, 19855105.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Zhang, X.4
  • 10
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 3146043, 20436464
    • 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.
    • (2010) Nat Biotechnol , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 11
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 14
    • 33847324900 scopus 로고    scopus 로고
    • Extensions to gene set enrichment
    • 10.1093/bioinformatics/btl599, 17127676
    • Jiang Z, Gentleman R. Extensions to gene set enrichment. Bioinformatics 2007, 23(3):306-313. 10.1093/bioinformatics/btl599, 17127676.
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 306-313
    • Jiang, Z.1    Gentleman, R.2
  • 15
    • 67649202800 scopus 로고    scopus 로고
    • GAGE: generally applicable gene set enrichment for pathway analysis
    • 10.1186/1471-2105-10-161, 2696452, 19473525
    • Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ. GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics 2009, 10:161. 10.1186/1471-2105-10-161, 2696452, 19473525.
    • (2009) BMC Bioinformatics , vol.10 , pp. 161
    • Luo, W.1    Friedman, M.S.2    Shedden, K.3    Hankenson, K.D.4    Woolf, P.J.5
  • 16
    • 84865777822 scopus 로고    scopus 로고
    • Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    • 10.1101/gr.134445.111, 3431479, 22955974
    • Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 2012, 22(9):1616-1625. 10.1101/gr.134445.111, 3431479, 22955974.
    • (2012) Genome Res , vol.22 , Issue.9 , pp. 1616-1625
    • Tilgner, H.1    Knowles, D.G.2    Johnson, R.3    Davis, C.A.4    Chakrabortty, S.5    Djebali, S.6    Curado, J.7    Snyder, M.8    Gingeras, T.R.9    Guigo, R.10
  • 18
    • 75849145292 scopus 로고    scopus 로고
    • Expansion of the eukaryotic proteome by alternative splicing
    • 10.1038/nature08909, 3443858, 20110989
    • Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature 2010, 463(7280):457-463. 10.1038/nature08909, 3443858, 20110989.
    • (2010) Nature , vol.463 , Issue.7280 , pp. 457-463
    • Nilsen, T.W.1    Graveley, B.R.2
  • 19
    • 1942454204 scopus 로고    scopus 로고
    • The impact of very short alternative splicing on protein structures and functions in the human genome
    • 10.1016/j.tig.2004.03.005, 15145575
    • Wen F, Li F, Xia H, Lu X, Zhang X, Li Y. The impact of very short alternative splicing on protein structures and functions in the human genome. Trends Genet 2004, 20(5):232-236. 10.1016/j.tig.2004.03.005, 15145575.
    • (2004) Trends Genet , vol.20 , Issue.5 , pp. 232-236
    • Wen, F.1    Li, F.2    Xia, H.3    Lu, X.4    Zhang, X.5    Li, Y.6
  • 20
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: diversification, exon definition and function
    • 10.1038/nrg2776, 20376054
    • Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010, 11(5):345-355. 10.1038/nrg2776, 20376054.
    • (2010) Nat Rev Genet , vol.11 , Issue.5 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 21
    • 84877047001 scopus 로고    scopus 로고
    • Statistical and computational methods for high throughput sequencing data analysis of alternative splicing
    • doi: 10.1007/s12561-012-9064-7
    • Chen L. Statistical and computational methods for high throughput sequencing data analysis of alternative splicing. Statistics in Biosciences 2012, doi: 10.1007/s12561-012-9064-7.
    • (2012) Statistics in Biosciences
    • Chen, L.1
  • 22
    • 77951940273 scopus 로고    scopus 로고
    • Modeling non-uniformity in short-read rates in RNA-Seq data
    • 10.1186/gb-2010-11-5-r50, 2898062, 20459815
    • Li J, Jiang H, Wong WH. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol 2010, 11(5):R50. 10.1186/gb-2010-11-5-r50, 2898062, 20459815.
    • (2010) Genome Biol , vol.11 , Issue.5
    • Li, J.1    Jiang, H.2    Wong, W.H.3
  • 23
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • 10.1093/bioinformatics/btp616, 2796818, 19910308
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26(1):139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 24
    • 77955298482 scopus 로고    scopus 로고
    • BaySeq: empirical Bayesian methods for identifying differential expression in sequence count data
    • 10.1186/1471-2105-11-422, 2928208, 20698981
    • Hardcastle TJ, Kelly KA. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010, 11:422. 10.1186/1471-2105-11-422, 2928208, 20698981.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 25
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • 10.1186/gb-2010-11-10-r106, 3218662, 20979621
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11(10):R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
    • (2010) Genome Biol , vol.11 , Issue.10
    • Anders, S.1    Huber, W.2
  • 26
    • 36448981743 scopus 로고    scopus 로고
    • Moderated statistical tests for assessing differences in tag abundance
    • 10.1093/bioinformatics/btm453, 17881408
    • Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 2007, 23(21):2881-2887. 10.1093/bioinformatics/btm453, 17881408.
    • (2007) Bioinformatics , vol.23 , Issue.21 , pp. 2881-2887
    • Robinson, M.D.1    Smyth, G.K.2
  • 27
    • 84875374758 scopus 로고    scopus 로고
    • Identifying differentially spliced genes from two groups of RNA-seq samples
    • doi: 10.1016/j.gene.2012.11.045
    • Wang W, Qin Z, Feng Z, Wang X, Zhang X. Identifying differentially spliced genes from two groups of RNA-seq samples. Gene 2012, doi: 10.1016/j.gene.2012.11.045.
    • (2012) Gene
    • Wang, W.1    Qin, Z.2    Feng, Z.3    Wang, X.4    Zhang, X.5
  • 28
    • 33845902772 scopus 로고    scopus 로고
    • Absolute enrichment: gene set enrichment analysis for homeostatic systems
    • 10.1093/nar/gkl766, 1702493, 17130162
    • Saxena V, Orgill D, Kohane I. Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res 2006, 34(22):e151. 10.1093/nar/gkl766, 1702493, 17130162.
    • (2006) Nucleic Acids Res , vol.34 , Issue.22
    • Saxena, V.1    Orgill, D.2    Kohane, I.3
  • 29
    • 84863453861 scopus 로고    scopus 로고
    • Technical and biological variance structure in mRNA-Seq data: life in the real world
    • 10.1186/1471-2164-13-304, 3505161, 22769017
    • Oberg AL, Bot BM, Grill DE, Poland GA, Therneau TM. Technical and biological variance structure in mRNA-Seq data: life in the real world. BMC Genomics 2012, 13(1):304. 10.1186/1471-2164-13-304, 3505161, 22769017.
    • (2012) BMC Genomics , vol.13 , Issue.1 , pp. 304
    • Oberg, A.L.1    Bot, B.M.2    Grill, D.E.3    Poland, G.A.4    Therneau, T.M.5
  • 30
    • 84868017347 scopus 로고    scopus 로고
    • GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
    • doi: 10.1093/bioinformatics/bts515
    • Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics 2012, doi: 10.1093/bioinformatics/bts515.
    • (2012) Bioinformatics
    • Feng, J.1    Meyer, C.A.2    Wang, Q.3    Liu, J.S.4    Liu, X.S.5    Zhang, Y.6
  • 31
    • 79959331609 scopus 로고    scopus 로고
    • Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing
    • 10.1073/pnas.1100489108, 3107329, 21571633
    • Kannan K, Wang L, Wang J, Ittmann MM, Li W, Yen L. Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proc Natl Acad Sci USA 2011, 108(22):9172-9177. 10.1073/pnas.1100489108, 3107329, 21571633.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.22 , pp. 9172-9177
    • Kannan, K.1    Wang, L.2    Wang, J.3    Ittmann, M.M.4    Li, W.5    Yen, L.6
  • 32
    • 85081776137 scopus 로고    scopus 로고
    • SRA
    • SRA. , http://www.ncbi.nlm.nih.gov/sra
  • 33
    • 85081782563 scopus 로고    scopus 로고
    • BA22 data URL
    • BA22 data URL. , http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1030
  • 34
    • 85081781826 scopus 로고    scopus 로고
    • HTSeq
    • HTSeq. , http://www-huber.embl.de/users/anders/HTSeq
  • 35
    • 85081782178 scopus 로고    scopus 로고
    • MSigDB
    • MSigDB. , http://www.broadinstitute.org/gsea/msigdb/index.jsp
  • 36
    • 33846467191 scopus 로고    scopus 로고
    • Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array
    • 10.1186/1471-2164-7-325, 1769375, 17192196
    • Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, et al. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 2006, 7:325. 10.1186/1471-2164-7-325, 1769375, 17192196.
    • (2006) BMC Genomics , vol.7 , pp. 325
    • Gardina, P.J.1    Clark, T.A.2    Shimada, B.3    Staples, M.K.4    Yang, Q.5    Veitch, J.6    Schweitzer, A.7    Awad, T.8    Sugnet, C.9    Dee, S.10
  • 37
    • 33646522416 scopus 로고    scopus 로고
    • Gene regulation by hypoxia and the neurodevelopmental origin of schizophrenia
    • 10.1016/j.schres.2006.02.022, 16632332
    • Schmidt-Kastner R, van Os J, H WMS, Schmitz C. Gene regulation by hypoxia and the neurodevelopmental origin of schizophrenia. Schizophr Res 2006, 84(2-3):253-271. 10.1016/j.schres.2006.02.022, 16632332.
    • (2006) Schizophr Res , vol.84 , Issue.2-3 , pp. 253-271
    • Schmidt-Kastner, R.1    van Os, J.2    H, W.M.S.3    Schmitz, C.4
  • 38
    • 33846573230 scopus 로고    scopus 로고
    • Phenylthiocarbamide (PTC) perception in patients with schizophrenia and first-degree family members: relationship to clinical symptomatology and psychophysical olfactory performance
    • 10.1016/j.schres.2006.11.014, 1862680, 17208411
    • Moberg PJ, McGue C, Kanes SJ, Roalf DR, Balderston CC, Gur RE, Kohler CG, Turetsky BI. Phenylthiocarbamide (PTC) perception in patients with schizophrenia and first-degree family members: relationship to clinical symptomatology and psychophysical olfactory performance. Schizophr Res 2007, 90(1-3):221-228. 10.1016/j.schres.2006.11.014, 1862680, 17208411.
    • (2007) Schizophr Res , vol.90 , Issue.1-3 , pp. 221-228
    • Moberg, P.J.1    McGue, C.2    Kanes, S.J.3    Roalf, D.R.4    Balderston, C.C.5    Gur, R.E.6    Kohler, C.G.7    Turetsky, B.I.8
  • 39
    • 85081778545 scopus 로고    scopus 로고
    • Association of schizophrenia with the phenylthiocarbamide taste receptor haplotype on chromosome 7q
    • doi: 10.1093/bioinformatics/bts515
    • Moberg PJ, Li M, Kanes SJ, Gur RE, Kamath V, Turetsky BI. Association of schizophrenia with the phenylthiocarbamide taste receptor haplotype on chromosome 7q. Psychiatr Genet 2012, doi: 10.1093/bioinformatics/bts515.
    • (2012) Psychiatr Genet
    • Moberg, P.J.1    Li, M.2    Kanes, S.J.3    Gur, R.E.4    Kamath, V.5    Turetsky, B.I.6
  • 40
    • 85081779290 scopus 로고    scopus 로고
    • IPA
    • IPA. , http://www.ingenuity.com/products/pathways_analysis.html
  • 41
    • 57149085481 scopus 로고    scopus 로고
    • Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    • 10.1093/nar/gkn705, 2588528, 18927111
    • 't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008, 36(21):e141. 10.1093/nar/gkn705, 2588528, 18927111.
    • (2008) Nucleic Acids Res , vol.36 , Issue.21
    • 'T Hoen, P.A.1    Ariyurek, Y.2    Thygesen, H.H.3    Vreugdenhil, E.4    Vossen, R.H.5    de Menezes, R.X.6    Boer, J.M.7    van Ommen, G.J.8    den Dunnen, J.T.9
  • 42
    • 79960914208 scopus 로고    scopus 로고
    • Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
    • 10.1038/ng.872, 21725310
    • Ju YS, Kim JI, Kim S, Hong D, Park H, Shin JY, Lee S, Lee WC, Yu SB, Park SS, et al. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet 2011, 43(8):745-752. 10.1038/ng.872, 21725310.
    • (2011) Nat Genet , vol.43 , Issue.8 , pp. 745-752
    • Ju, Y.S.1    Kim, J.I.2    Kim, S.3    Hong, D.4    Park, H.5    Shin, J.Y.6    Lee, S.7    Lee, W.C.8    Yu, S.B.9    Park, S.S.10
  • 44
    • 79960208246 scopus 로고    scopus 로고
    • Sequencing technology does not eliminate biological variability
    • 10.1038/nbt.1910, 3137276, 21747377
    • Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nat Biotechnol 2011, 29(7):572-573. 10.1038/nbt.1910, 3137276, 21747377.
    • (2011) Nat Biotechnol , vol.29 , Issue.7 , pp. 572-573
    • Hansen, K.D.1    Wu, Z.2    Irizarry, R.A.3    Leek, J.T.4
  • 45
    • 79951522882 scopus 로고    scopus 로고
    • Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
    • 10.1093/bioinformatics/btq696, 21169371
    • Wu Z, Wang X, Zhang X. Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics 2011, 27(4):502-508. 10.1093/bioinformatics/btq696, 21169371.
    • (2011) Bioinformatics , vol.27 , Issue.4 , pp. 502-508
    • Wu, Z.1    Wang, X.2    Zhang, X.3


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