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Volumn 5, Issue , 2015, Pages

Efficient Test and Visualization of Multi-Set Intersections

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER INTERFACE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN; INTERNET; NEOPLASM; PATHOLOGY; PHENOTYPE; THEORETICAL MODEL;

EID: 84948174122     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep16923     Document Type: Article
Times cited : (273)

References (45)
  • 1
    • 84862216273 scopus 로고    scopus 로고
    • GeneSigDB: A manually curated database and resource for analysis of gene expression signatures
    • Culhane, A. C. et al. GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Research 40, D1060-D1066 (2012).
    • (2012) Nucleic Acids Research , vol.40 , pp. D1060-D1066
    • Culhane, A.C.1
  • 2
    • 34447555782 scopus 로고    scopus 로고
    • Mining gene expression profiles: Expression signatures as cancer phenotypes
    • Nevins, J. R. & Potti, A. Mining gene expression profiles: expression signatures as cancer phenotypes. Nat Rev Genet 8, 601-609 (2007).
    • (2007) Nat Rev Genet , vol.8 , pp. 601-609
    • Nevins, J.R.1    Potti, A.2
  • 3
    • 0002969802 scopus 로고
    • A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons
    • Sørensen, T. A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Biologiske skrifter 5, 1-34 (1948).
    • (1948) Biologiske Skrifter , vol.5 , pp. 1-34
    • Sørensen, T.1
  • 4
    • 84980090975 scopus 로고
    • The distribution of the flora in the alpine zone
    • Jaccard, P. The distribution of the flora in the alpine zone. New Phytologist 11, 37-50 (1912).
    • (1912) New Phytologist , vol.11 , pp. 37-50
    • Jaccard, P.1
  • 5
    • 0002386913 scopus 로고
    • On the Interpretation of χ2 from Contingency Tables, and the Calculation of P
    • Fisher, R. A. On the Interpretation of χ2 from Contingency Tables, and the Calculation of P. Journal of the Royal Statistical Society 85, 87-94 (1922).
    • (1922) Journal of the Royal Statistical Society , vol.85 , pp. 87-94
    • Fisher, R.A.1
  • 7
    • 33847264343 scopus 로고    scopus 로고
    • Enrichment or depletion of a GO category within a class of genes: Which test ?
    • Rivals, I., Personnaz, L., Taing, L. & Potier, M.-C. Enrichment or depletion of a GO category within a class of genes: which test ? Bioinformatics 23, 401-407 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 401-407
    • Rivals, I.1    Personnaz, L.2    Taing, L.3    Potier, M.-C.4
  • 8
    • 0037474153 scopus 로고    scopus 로고
    • Joint mathematics meetings. Diagram masters cry 'Venn-i, vidi, vici'
    • Cipra, B. Joint mathematics meetings. Diagram masters cry 'Venn-i, vidi, vici'. Science 299, 651 (2003).
    • (2003) Science , vol.299 , pp. 651
    • Cipra, B.1
  • 9
    • 42449094561 scopus 로고    scopus 로고
    • VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays
    • Kestler, H. A. et al. VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9, 67 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 67
    • Kestler, H.A.1
  • 10
    • 17444417122 scopus 로고    scopus 로고
    • Generalized Venn diagrams: A new method of visualizing complex genetic set relations
    • Kestler, H. A., Muller, A., Gress, T. M. & Buchholz, M. Generalized Venn diagrams: a new method of visualizing complex genetic set relations. Bioinformatics 21, 1592-1595 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 1592-1595
    • Kestler, H.A.1    Muller, A.2    Gress, T.M.3    Buchholz, M.4
  • 11
    • 83855162851 scopus 로고    scopus 로고
    • Exact and approximate area-proportional circular Venn and Euler diagrams
    • Wilkinson, L. Exact and approximate area-proportional circular Venn and Euler diagrams. IEEE Trans on Visual and Comp Graph 18, 321-331 (2012).
    • (2012) IEEE Trans on Visual and Comp Graph , vol.18 , pp. 321-331
    • Wilkinson, L.1
  • 12
    • 84905259752 scopus 로고    scopus 로고
    • Points of view: Sets and intersections
    • Lex, A. & Gehlenborg, N. Points of view: Sets and intersections. Nat Meth 11, 779-779 (2014).
    • (2014) Nat Meth , vol.11 , pp. 779-779
    • Lex, A.1    Gehlenborg, N.2
  • 13
    • 79251555660 scopus 로고    scopus 로고
    • VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R
    • Chen, H. & Boutros, P. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12, 35 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 35
    • Chen, H.1    Boutros, P.2
  • 14
    • 83855162851 scopus 로고    scopus 로고
    • Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams
    • Leland, W. Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams. IEEE Trans on Visual and Comp Graph 18, 321-331 (2012).
    • (2012) IEEE Trans on Visual and Comp Graph , vol.18 , pp. 321-331
    • Leland, W.1
  • 15
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. Genome Research 19, 1639-1645 (2009).
    • (2009) Genome Research , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 16
    • 1542515338 scopus 로고    scopus 로고
    • A census of human cancer genes
    • Futreal, P. A. et al. A census of human cancer genes. Nat Rev Cancer 4, 177-183 (2004).
    • (2004) Nat Rev Cancer , vol.4 , pp. 177-183
    • Futreal, P.A.1
  • 17
    • 84892833777 scopus 로고    scopus 로고
    • Discovery and saturation analysis of cancer genes across 21 tumour types
    • Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501 (2014).
    • (2014) Nature , vol.505 , pp. 495-501
    • Lawrence, M.S.1
  • 18
    • 84892607343 scopus 로고    scopus 로고
    • Realizing the promise of cancer predisposition genes
    • Rahman, N. Realizing the promise of cancer predisposition genes. Nature 505, 302-308 (2014).
    • (2014) Nature , vol.505 , pp. 302-308
    • Rahman, N.1
  • 19
    • 84885735554 scopus 로고    scopus 로고
    • Mutational landscape and significance across 12 major cancer types
    • Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333-339 (2013).
    • (2013) Nature , vol.502 , pp. 333-339
    • Kandoth, C.1
  • 20
    • 84875758730 scopus 로고    scopus 로고
    • Lessons from the cancer genome
    • Garraway, L. A. & Lander, E. S. Lessons from the cancer genome. Cell 153, 17-37 (2013).
    • (2013) Cell , vol.153 , pp. 17-37
    • Garraway, L.A.1    Lander, E.S.2
  • 21
    • 84875490185 scopus 로고    scopus 로고
    • Cancer genome landscapes
    • Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
    • (2013) Science , vol.339 , pp. 1546-1558
    • Vogelstein, B.1
  • 22
    • 84885129618 scopus 로고    scopus 로고
    • Comprehensive identification of mutational cancer driver genes across 12 tumor types
    • Tamborero, D. et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific Reports 3, 2650 (2013).
    • (2013) Scientific Reports , vol.3 , pp. 2650
    • Tamborero, D.1
  • 23
    • 84876907931 scopus 로고    scopus 로고
    • Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer's Disease
    • Zhang, B. et al. Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer's Disease. Cell 153, 707-720 (2013).
    • (2013) Cell , vol.153 , pp. 707-720
    • Zhang, B.1
  • 24
    • 47649132153 scopus 로고    scopus 로고
    • Programmed genetic instability: A tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line
    • Zhao, Y. & Epstein, R. J. Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line. Mol Biol Evol 25, 1737-1749 (2008).
    • (2008) Mol Biol Evol , vol.25 , pp. 1737-1749
    • Zhao, Y.1    Epstein, R.J.2
  • 25
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • Hindorff, L. A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106, 9362-9367 (2009).
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1
  • 26
    • 84879324656 scopus 로고    scopus 로고
    • Pitfalls of predicting complex traits from SNPs
    • Wray, N. R. et al. Pitfalls of predicting complex traits from SNPs. Nat Rev Genet 14, 507-515 (2013).
    • (2013) Nat Rev Genet , vol.14 , pp. 507-515
    • Wray, N.R.1
  • 28
    • 84875238532 scopus 로고    scopus 로고
    • Semaphorins 3A and 7A: Potential immune and neuroregenerative targets in multiple sclerosis
    • Eixarch, H., Gutierrez-Franco, A., Montalban, X. & Espejo, C. Semaphorins 3A and 7A: potential immune and neuroregenerative targets in multiple sclerosis. Trends in Molecular Medicine 19, 157-164 (2013).
    • (2013) Trends in Molecular Medicine , vol.19 , pp. 157-164
    • Eixarch, H.1    Gutierrez-Franco, A.2    Montalban, X.3    Espejo, C.4
  • 29
    • 84905491435 scopus 로고    scopus 로고
    • Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease
    • Makinen, V. P. et al. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet 10, e1004502 (2014).
    • (2014) PLoS Genet , vol.10
    • Makinen, V.P.1
  • 30
    • 84906306427 scopus 로고    scopus 로고
    • Complex disease: Piecing together the puzzle of coronary artery disease
    • Lau, E. Complex disease: Piecing together the puzzle of coronary artery disease. Nat Rev Genet 15, 572-573 (2014).
    • (2014) Nat Rev Genet , vol.15 , pp. 572-573
    • Lau, E.1
  • 31
    • 84904806049 scopus 로고    scopus 로고
    • RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration
    • Ishimura, R. et al. RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science 345, 455-459 (2014).
    • (2014) Science , vol.345 , pp. 455-459
    • Ishimura, R.1
  • 32
    • 84899581919 scopus 로고    scopus 로고
    • CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration
    • Schaffer, A. E. et al. CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Cell 157, 651-663 (2014).
    • (2014) Cell , vol.157 , pp. 651-663
    • Schaffer, A.E.1
  • 33
    • 40749105508 scopus 로고    scopus 로고
    • Variations in DNA elucidate molecular networks that cause disease
    • Chen, Y. et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-435 (2008).
    • (2008) Nature , vol.452 , pp. 429-435
    • Chen, Y.1
  • 34
    • 41349095280 scopus 로고    scopus 로고
    • Genetics of gene expression and its effect on disease
    • Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423-428 (2008).
    • (2008) Nature , vol.452 , pp. 423-428
    • Emilsson, V.1
  • 35
    • 84255175411 scopus 로고    scopus 로고
    • Obesity, leptin, and Alzheimer's disease
    • Lee, E. B. Obesity, leptin, and Alzheimer's disease. Ann N Y Acad Sci 1243, 15-29 (2011).
    • (2011) Ann N Y Acad Sci , vol.1243 , pp. 15-29
    • Lee, E.B.1
  • 36
    • 84864208657 scopus 로고    scopus 로고
    • Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers
    • Wang, I. M. et al. Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers. Mol Syst Biol 8, 594 (2012).
    • (2012) Mol Syst Biol , vol.8 , pp. 594
    • Wang, I.M.1
  • 37
    • 84866262639 scopus 로고    scopus 로고
    • Statistical tests for the intersection of independent lists of genes: Sensitivity, FDR, and type I error control
    • Natarajan, P. Statistical tests for the intersection of independent lists of genes: Sensitivity, FDR, and type I error control. The Annals of Applied Statistics 6, 521-541 (2012).
    • (2012) The Annals of Applied Statistics , vol.6 , pp. 521-541
    • Natarajan, P.1
  • 38
    • 84965695261 scopus 로고
    • An Exact Significance Test for Three-Way Interaction Effects
    • White, D. R., Pesner, R. & Reitz, K. P. An Exact Significance Test for Three-Way Interaction Effects. Cross-Cultural Research 18, 103-122 (1983).
    • (1983) Cross-Cultural Research , vol.18 , pp. 103-122
    • White, D.R.1    Pesner, R.2    Reitz, K.P.3
  • 39
    • 84897671878 scopus 로고    scopus 로고
    • Exact inference in contingency tables via stochastic approximation Monte Carlo
    • Jung, B. C., So, S. & Cheon, S. Exact inference in contingency tables via stochastic approximation Monte Carlo. J of the Kor Stat Soc 43, 31-45 (2014).
    • (2014) J of the Kor Stat Soc , vol.43 , pp. 31-45
    • Jung, B.C.1    So, S.2    Cheon, S.3
  • 40
    • 0000993098 scopus 로고
    • Contingency Tables Involving Small Numbers and the χ2 Test
    • Yates, F. Contingency Tables Involving Small Numbers and the χ2 Test. Supplement to the J of the Roy Stat Soc 1, 217-235 (1934).
    • (1934) Supplement to the J of the Roy Stat Soc , vol.1 , pp. 217-235
    • Yates, F.1
  • 41
    • 0001677717 scopus 로고
    • Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    • Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J of the Roy Stat Soc. Series B (Methodological) 57, 289-300 (1995).
    • (1995) J of the Roy Stat Soc. Series B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 42
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95, 14863-14868 (1998).
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 43
    • 84883812062 scopus 로고    scopus 로고
    • Network link prediction by global silencing of indirect correlations
    • Barzel, B. & Barabasi, A.-L. Network link prediction by global silencing of indirect correlations. Nat Biotech 31, 720-725 (2013).
    • (2013) Nat Biotech , vol.31 , pp. 720-725
    • Barzel, B.1    Barabasi, A.-L.2
  • 44
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
    • Shannon, P. et al. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13, 2498-2504 (2003).
    • (2003) Genome Research , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 45
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner, L. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286 (1989).
    • (1989) Proceedings of the IEEE , vol.77 , pp. 257-286
    • Rabiner, L.1


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