메뉴 건너뛰기




Volumn 44, Issue 1, 2016, Pages e1-

ROTS: Reproducible RNA-seq biomarker detector - Prognostic markers for clear cell renal cell cancer

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE TRANSPORTER 2; TUMOR MARKER;

EID: 84959452344     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv806     Document Type: Article
Times cited : (42)

References (39)
  • 1
    • 84920550975 scopus 로고    scopus 로고
    • A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
    • Seqc/Maqc-Iii Consortium. (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat. Biotechnol., 32, 903-914.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 903-914
  • 5
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson,M.D., McCarthy,D.J. and Smyth,G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinforma. Oxf. Engl., 26, 139-140.
    • (2010) Bioinforma. Oxf. Engl. , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 6
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • McCarthy,D.J., Chen,Y. and Smyth,G.K. (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res., 40, 4288-4297.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.2    Smyth, G.K.3
  • 7
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders,S. and Huber,W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 8
    • 77955298482 scopus 로고    scopus 로고
    • baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle,T.J. and Kelly,K.A. (2010) baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 10
    • 84928199480 scopus 로고    scopus 로고
    • Comparison of software packages for detecting differential expression in RNA-seq studies
    • Seyednasrollah,F., Laiho,A. and Elo,L.L. (2015) Comparison of software packages for detecting differential expression in RNA-seq studies. Brief. Bioinform., 16,59-70.
    • (2015) Brief. Bioinform. , vol.16 , pp. 59-70
    • Seyednasrollah, F.1    Laiho, A.2    Elo, L.L.3
  • 12
    • 84874677498 scopus 로고    scopus 로고
    • A comparison of methods for differential expression analysis of RNA-seq data
    • Soneson,C. and Delorenzi,M. (2013) A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics, 14, 91.
    • (2013) BMC Bioinformatics , vol.14 , pp. 91
    • Soneson, C.1    Delorenzi, M.2
  • 14
    • 69249105669 scopus 로고    scopus 로고
    • Optimized detection of differential expression in global profiling experiments: Case studies in clinical transcriptomic and quantitative proteomic datasets
    • Elo,L.L., Hiissa,J., Tuimala,J., Kallio,A., Korpelainen,E. and Aittokallio,T. (2009) Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Brief. Bioinform., 10, 547-555.
    • (2009) Brief. Bioinform. , vol.10 , pp. 547-555
    • Elo, L.L.1    Hiissa, J.2    Tuimala, J.3    Kallio, A.4    Korpelainen, E.5    Aittokallio, T.6
  • 16
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim,D., Pertea,G., Trapnell,C., Pimentel,H., Kelley,R. and Salzberg,S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 17
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq - A Python framework to work with high-throughput sequencing data
    • Anders,S., Pyl,P.T. and Huber,W. (2015) HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 18
    • 84879890360 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of clear cell renal cell carcinoma
    • The Cancer Genome Atlas Research Network. (2013) Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature, 499, 43-49.
    • (2013) Nature , vol.499 , pp. 43-49
    • The Cancer Genome Atlas Research Network1
  • 20
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard,J.H., Purdom,E., Hansen,K.D. and Dudoit,S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4
  • 22
    • 84896735766 scopus 로고    scopus 로고
    • voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law,C.W., Chen,Y., Shi,W. and Smyth,G.K. (2014) voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol., 15, R29.
    • (2014) Genome Biol. , vol.15 , pp. R29
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 23
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher,V.G., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A., 98, 5116-5121.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 25
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love,M.I., Huber,W. and Anders,S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 26
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth,G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article3.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 27
    • 84926507971 scopus 로고    scopus 로고
    • limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie,M.E., Phipson,B., Wu,D., Hu,Y., Law,C.W., Shi,W. and Smyth,G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47-e47.
    • (2015) Nucleic Acids Res. , vol.43 , pp. e47-e47
    • Ritchie, M.E.1    Phipson, B.2    Wu, D.3    Hu, Y.4    Law, C.W.5    Shi, W.6    Smyth, G.K.7
  • 28
    • 84863562292 scopus 로고    scopus 로고
    • Normalization, testing, and false discovery rate estimation for RNA-sequencing data
    • Li,J., Witten,D.M., Johnstone,I.M. and Tibshirani,R. (2012) Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostat. Oxf. Engl., 13, 523-538.
    • (2012) Biostat. Oxf. Engl. , vol.13 , pp. 523-538
    • Li, J.1    Witten, D.M.2    Johnstone, I.M.3    Tibshirani, R.4
  • 31
    • 70449521466 scopus 로고    scopus 로고
    • External validation of the Mayo Clinic stage, size, grade, and necrosis (SSIGN) score for clear-cell renal cell carcinoma in a single European centre applying routine pathology
    • Zigeuner,R., Hutterer,G., Chromecki,T., Imamovic,A., Kampel-Kettner,K., Rehak,P., Langner,C. and Pummer,K. (2010) External validation of the Mayo Clinic stage, size, grade, and necrosis (SSIGN) score for clear-cell renal cell carcinoma in a single European centre applying routine pathology. Eur. Urol., 57, 102-109.
    • (2010) Eur. Urol. , vol.57 , pp. 102-109
    • Zigeuner, R.1    Hutterer, G.2    Chromecki, T.3    Imamovic, A.4    Kampel-Kettner, K.5    Rehak, P.6    Langner, C.7    Pummer, K.8
  • 32
    • 38049169977 scopus 로고    scopus 로고
    • Surveillance strategies for renal cell carcinoma patients following nephrectomy
    • Chin,A.I., Lam,J.S., Figlin,R.A. and Belldegrun,A.S. (2006) Surveillance strategies for renal cell carcinoma patients following nephrectomy. Rev. Urol., 8, 1-7.
    • (2006) Rev. Urol. , vol.8 , pp. 1-7
    • Chin, A.I.1    Lam, J.S.2    Figlin, R.A.3    Belldegrun, A.S.4
  • 37
    • 84873081430 scopus 로고    scopus 로고
    • Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: A retrospective analysis with independent validation
    • Kapur,P., Peña-Llopis,S., Christie,A., Zhrebker,L., Pavía-Jiménez,A., Rathmell,W.K., Xie,X.-J. and Brugarolas,J. (2013) Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation. Lancet Oncol., 14, 159-167.
    • (2013) Lancet Oncol. , vol.14 , pp. 159-167
    • Kapur, P.1    Peña-Llopis, S.2    Christie, A.3    Zhrebker, L.4    Pavía-Jiménez, A.5    Rathmell, W.K.6    Xie, X.-J.7    Brugarolas, J.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.