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Volumn 46, Issue 9, 2018, Pages

Improving the value of public RNA-seq expression data by phenotype prediction

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; CONTROLLED STUDY; CORRELATIONAL STUDY; FEMALE; GENE EXPRESSION; GENETIC ASSOCIATION; GENOMICS; HUMAN; HUMAN TISSUE; MALE; MIDDLE AGED; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEX CHROMOSOME; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; SOFTWARE;

EID: 85061812937     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gky102     Document Type: Article
Times cited : (37)

References (31)
  • 2
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi,U., Wang,Z., Waern,K., Shou,C., Raha,D., Gerstein,M. and Snyder,M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344–1349.
    • (2008) SCIENCE , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 8
    • 85014594340 scopus 로고    scopus 로고
    • Don’t let useful data go to waste
    • Denk,F. (2017) Don’t let useful data go to waste. Nat. News, 543, 7.
    • (2017) Nat. News , vol.543 , pp. 7
    • Denk, F.1
  • 11
    • 34848914038 scopus 로고    scopus 로고
    • Capturing heterogeneity in gene expression studies by surrogate variable analysis
    • Leek,J.T. and Storey,J.D. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet., 3, 1724–1735.
    • (2007) PLoS Genet. , vol.3 , pp. 1724-1735
    • Leek, J.T.1    Storey, J.D.2
  • 13
    • 84929001104 scopus 로고    scopus 로고
    • The Genotype-Tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
    • Consortium,T.G. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348, 648–660.
    • (2015) SCIENCE , vol.348 , pp. 648-660
    • Consortium, T.G.1
  • 14
    • 85029793308 scopus 로고    scopus 로고
    • MetaSRA: Normalized human sample-specific metadata for the Sequence Read Archive
    • Bernstein,M.N., Doan,A. and Dewey,C.N. (2017) MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bioinformatics, 33, 2914–2923.
    • (2017) Bioinformatics , vol.33 , pp. 2914-2923
    • Bernstein, M.N.1    Doan, A.2    Dewey, C.N.3
  • 15
    • 78649903173 scopus 로고    scopus 로고
    • Sex bias in neuroscience and biomedical research
    • Beery,A.K. and Zucker,I. (2011) Sex bias in neuroscience and biomedical research. Neurosci. Biobehav. Rev., 35, 565–572.
    • (2011) Neurosci Biobehav Rev , vol.35 , pp. 565-572
    • Beery, A.K.1    Zucker, I.2
  • 16
    • 84958904696 scopus 로고    scopus 로고
    • Twenty years and still counting: Including women as participants and studying sex and gender in biomedical research
    • Mazure,C.M. and Jones,D.P. (2015) Twenty years and still counting: including women as participants and studying sex and gender in biomedical research. BMC Women’s Health, 15, 94.
    • (2015) BMC Womens Health , vol.15 , pp. 94
    • Mazure, C.M.1    Jones, D.P.2
  • 18
    • 84901358543 scopus 로고    scopus 로고
    • BWTool: A tool for bigwig files
    • Pohl,A. and Beato,M. (2014) bwtool: a tool for bigWig files. Bioinformatics, 30, 1618–1619.
    • (2014) Bioinformatics , vol.30 , pp. 1618-1619
    • Pohl, A.1    Beato, M.2
  • 19
    • 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.
    • (2015) Nucleic Acids Res , vol.43 , pp. 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
  • 22
    • 84893772701 scopus 로고    scopus 로고
    • RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma
    • Smallridge,R.C., Chindris,A.-M., Asmann,Y.W., Casler,J.D., Serie,D.J., Reddi,H.V., Cradic,K.W., Rivera,M., Grebe,S.K., Necela,B.M. et al. (2014) RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma. J. Clin. Endocrinol. Metab., 99, E338–E347.
    • (2014) J Clin Endocrinol Metab , vol.99 , pp. E338-E347
    • Smallridge, R.C.1    Chindris, A.-M.2    Asmann, Y.W.3    Casler, J.D.4    Serie, D.J.5    Reddi, H.V.6    Cradic, K.W.7    Rivera, M.8    Grebe, S.K.9    Necela, B.M.10
  • 23
    • 84911961534 scopus 로고    scopus 로고
    • A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients
    • Kim,S.-K., Kim,S.-Y., Kim,J.-H., Roh,S.A., Cho,D.-H., Kim,Y.S. and Kim,J.C. (2014) A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients. Mol. Oncol., 8, 1653–1666.
    • (2014) Mol Oncol , vol.8 , pp. 1653-1666
    • Kim, S.-K.1    Kim, S.-Y.2    Kim, J.-H.3    Roh, S.A.4    Cho, D.-H.5    Kim, Y.S.6    Kim, J.C.7
  • 24
    • 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. Bioinformatics, 26, 139–140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 25
    • 46049110099 scopus 로고    scopus 로고
    • TiGER: A database for tissue-specific gene expression and regulation
    • Liu,X., Yu,X., Zack,D.J., Zhu,H. and Qian,J. (2008) TiGER: A database for tissue-specific gene expression and regulation. BMC Bioinformatics, 9, 271.
    • (2008) BMC Bioinformatics , vol.9 , pp. 271
    • Liu, X.1    Yu, X.2    Zack, D.J.3    Zhu, H.4    Qian, J.5
  • 27
    • 85010952398 scopus 로고    scopus 로고
    • Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies
    • Toker,L., Feng,M. and Pavlidis,P. (2016) Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies. F1000Research, 5, 2103.
    • (2016) F1000Research , vol.5 , pp. 2103
    • Toker, L.1    Feng, M.2    Pavlidis, P.3
  • 28
    • 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
  • 30
    • 84954548507 scopus 로고    scopus 로고
    • Tumor-derived cell lines as molecular models of cancer pharmacogenomics
    • Goodspeed,A., Heiser,L.M., Gray,J.W. and Costello,J.C. (2016) Tumor-derived cell lines as molecular models of cancer pharmacogenomics. Mol. Cancer Res.: MCR, 14, 3–13.
    • (2016) Mol. Cancer Res.: MCR , vol.14 , pp. 3-13
    • Goodspeed, A.1    Heiser, L.M.2    Gray, J.W.3    Costello, J.C.4


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