$\require{mediawiki-texvc}$

연합인증

연합인증 가입 기관의 연구자들은 소속기관의 인증정보(ID와 암호)를 이용해 다른 대학, 연구기관, 서비스 공급자의 다양한 온라인 자원과 연구 데이터를 이용할 수 있습니다.

이는 여행자가 자국에서 발행 받은 여권으로 세계 각국을 자유롭게 여행할 수 있는 것과 같습니다.

연합인증으로 이용이 가능한 서비스는 NTIS, DataON, Edison, Kafe, Webinar 등이 있습니다.

한번의 인증절차만으로 연합인증 가입 서비스에 추가 로그인 없이 이용이 가능합니다.

다만, 연합인증을 위해서는 최초 1회만 인증 절차가 필요합니다. (회원이 아닐 경우 회원 가입이 필요합니다.)

연합인증 절차는 다음과 같습니다.

최초이용시에는
ScienceON에 로그인 → 연합인증 서비스 접속 → 로그인 (본인 확인 또는 회원가입) → 서비스 이용

그 이후에는
ScienceON 로그인 → 연합인증 서비스 접속 → 서비스 이용

연합인증을 활용하시면 KISTI가 제공하는 다양한 서비스를 편리하게 이용하실 수 있습니다.

Visualization of SNPs with t-SNE 원문보기

PloS one, v.8 no.2, 2013년, pp.e56883 -   

Platzer, Alexander (Gregor Mendel Institute, Vienna, Austria)

Abstract AI-Helper 아이콘AI-Helper

BackgroundSingle Nucleotide Polymorphisms (SNPs) are one of the largest sources of new data in biology. In most papers, SNPs between individuals are visualized with Principal Component Analysis (PCA), an older method for this purpose.Principal FindingsWe compare PCA, an aging method for this purpose...

참고문헌 (45)

  1. 1 Pearson K ( 1901 ) On Lines and Planes of Closest Fit to Systems of Points in Space . Philosophical Magazine 2 : 559 – 572 . 

  2. 2 Sun Z , Chai HS , Wu Y , White WM , Donkena KV , et al ( 2011 ) Batch effect correction for genome-wide methylation data with Illumina Infinium platform . BMC Med Genomics 4 : 84 . 22171553 

  3. 3 Swingley WD , Meyer-Dombard DR , Shock EL , Alsop EB , Falenski HD , et al ( 2012 ) Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem . PLoS One 7 : e38108 . 22675512 

  4. 4 Zhou H , Muehlbauer G , Steffenson B ( 2012 ) Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States . J Zhejiang Univ Sci B 13 : 438 – 451 . 22661207 

  5. 5 Hurtado MA , Racotta IS , Arcos F , Morales-Bojorquez E , Moal J , et al ( 2012 ) Seasonal variations of biochemical, pigment, fatty acid, and sterol compositions in female Crassostrea corteziensis oysters in relation to the reproductive cycle . Comp Biochem Physiol B Biochem Mol Biol 

  6. 6 Jarzynska G , Falandysz J ( 2011 ) Selenium and 17 other largely essential and toxic metals in muscle and organ meats of Red Deer (Cervus elaphus)–consequences to human health . Environ Int 37 : 882 – 888 . 21429582 

  7. 7 Yu Z , Tan BK , Dainty S , Mattey DL , Davies SJ ( 2012 ) Hypoalbuminaemia, systemic albumin leak and endothelial dysfunction in peritoneal dialysis patients . Nephrol Dial Transplant 

  8. 8 A Tutorial on Principal Component Analysis. Available: http://www.snl.salk.edu/~shlens/pca.pdf . Accessed: 2013 Jan 21. 

  9. 9 Lu H , Plataniotis KN , Venetsanopoulos AN ( 2008 ) MPCA: Multilinear Principal Component Analysis of Tensor Objects . IEEE Trans Neural Netw 19 : 18 – 39 . 18269936 

  10. 10 Bellman RE (1961) Adaptive Control Processes. Princeton, NJ: Princeton University Press. 

  11. 11 Sammon JW ( 1969 ) A Nonlinear Mapping for Data Structure Analysis . Ieee Transactions on Computers C 18 : 401-& . 

  12. 12 Tenenbaum JB , de Silva V , Langford JC ( 2000 ) A global geometric framework for nonlinear dimensionality reduction . Science 290 : 2319-+ . 11125149 

  13. 13 Roweis ST , Saul LK ( 2000 ) Nonlinear dimensionality reduction by locally linear embedding . Science 290 : 2323 – 2326 . 11125150 

  14. 14 Torgerson WS ( 1952 ) Multidimensional Scaling: I. Theory and Method . Psychometrika 17 : 401 – 419 . 

  15. 15 Belkin M , Niyogi P ( 2002 ) Laplacian eigenmaps and spectral techniques for embedding and clustering . Advances in Neural Information Processing Systems 14, Vols 1 and 2 14 : 585 – 591 . 

  16. 16 Xie B , Mu Y , Tao DC ( 2010 ) m-SNE: Multiview Stochastic Neighbor Embedding . Neural Information Processing: Theory and Algorithms, Pt I 6443 : 338 – 346 . 

  17. 17 van der Maaten L , Hinton G ( 2008 ) Visualizing Data using t-SNE . Journal of Machine Learning Research 9 : 2579 – 2605 . 

  18. 18 Dunn JC ( 1973 ) A Fuzzy Relative of the ISODATA Process and Its Use in Detecting Compact Well-Separated Clusters . Journal of Cybernetics 3 : 32 – 57 . 

  19. 19 Rousseeuw PJ ( 1987 ) Silhouettes - a Graphical Aid to the Interpretation and Validation of Cluster-Analysis . Journal of Computational and Applied Mathematics 20 : 53 – 65 . 

  20. 20 Halkidi M , Batistakis Y , Vazirgiannis M ( 2001 ) On clustering validation techniques . Journal of Intelligent Information Systems 17 : 107 – 145 . 

  21. 21 Quinlan JR (1993) Programs for Machine Learning: Morgan Kaufmann Publishers. 

  22. 22 Rumelhart DE, Geoffrey E Hinton, and R. J Williams (1986) Learning Internal Representations by Error Propagation. In: Parallel distributed processing: Explorations in the microstructure of cognition. Cambridge: MIT Press. pp. 318–362. 

  23. 23 Frank E, Witten I. Generating Accurate Rule Sets Without Global Optimization; 1998; Shavlik. Morgan Kaufmann Publishers, San Francisco, CA. 

  24. 24 Zhang H ( 2005 ) Exploring conditions for the optimality of Naive bayes . International Journal of Pattern Recognition and Artificial Intelligence 19 : 183 – 198 . 

  25. 25 Weigel D , Mott R ( 2009 ) The 1001 Genomes Project for Arabidopsis thaliana . Genome Biology 10 . 

  26. 26 Horton MW , Hancock AM , Huang YS , Toomajian C , Atwell S , et al ( 2012 ) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel . Nature Genetics 44 : 212 – 216 . 22231484 

  27. 27 Altshuler DM , Gibbs RA , Peltonen L , Dermitzakis E , Schaffner SF , et al ( 2010 ) Integrating common and rare genetic variation in diverse human populations . Nature 467 : 52 – 58 . 20811451 

  28. 28 Huang X , Kurata N , Wei X , Wang ZX , Wang A , et al ( 2012 ) A map of rice genome variation reveals the origin of cultivated rice . Nature 490 : 497 – 501 . 23034647 

  29. 29 Khalilia M , Chakraborty S , Popescu M ( 2011 ) Predicting disease risks from highly imbalanced data using random forest . Bmc Medical Informatics and Decision Making 11 . 

  30. 30 Lin WJ , Chen JJ ( 2012 ) Class-imbalanced classifiers for high-dimensional data . Brief Bioinform 

  31. 31 Nothnagel M , Lu TT , Kayser M , Krawczak M ( 2010 ) Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans . Hum Mol Genet 19 : 2927 – 2935 . 20462934 

  32. 32 Sharbel TF , Haubold B , Mitchell-Olds T ( 2000 ) Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe . Mol Ecol 9 : 2109 – 2118 . 11123622 

  33. 33 Laurens van der Maaten EP, Jaap van den Herik (2009) Dimensionality Reduction: A Comparative Review. Tilburg: Tilburg University. 

  34. 34 Asuncion AFaA (2010) UCI Machine Learning Repository. University of California, Irvine, School of Information and Computer Sciences. 

  35. 35 Christopher D. Manning PR, Hinrich Schütze (2009) An Introduction to Information Retrieval. Cambridge, England: Cambridge University Press. 

  36. 36 Amir Globerson NT ( 2003 ) Sufficient Dimensionality Reduction . Machine Learning Research 3 : 1307 – 1331 . 

  37. 37 Ackerman M, Ben-David S. Clusterability: A Theoretical Study; 2009; Clearwater Beach, Florida, USA. 

  38. 38 Pau G ( 2010 ) Clustering and classification with applications to microarrays and cellular phenotypes . Bressanone-Brixen, Italy: Computational Statistics for Genome Biology 2010 . 

  39. 39 t-Distributed Stochastic Neighbor Embedding - Implementations. Available: http://homepage.tudelft.nl/19j49/t-SNE.html . Accessed: 21 June 2012. 

  40. 40 Brown PL , Della Pietra V , Lai JC , Mercer RL ( 1992 ) An estimate of an upper bound for the entropy of English . Computational Linguistics 18 : 31 – 40 . 

  41. 41 Dunn index – Wikipedia, The Free Encyclopedia. Available: http://en.wikipedia.org/w/index.php?title=Dunn_index&oldid=511861769 . Accessed: 7 Jan 2013. 

  42. 42 Silhouette (clustering) – Wikipedia, The Free Encyclopedia. Available: http://en.wikipedia.org/w/index.php?title=Silhouette_(clustering)&oldid=528712368 . Accessed: 2013 Jan 7. 

  43. 43 Tibshirani R , Walther G , Hastie T ( 2000 ) Estimating the number of clusters in a dataset via the Gap statistic . 63 : 411 – 423 . 

  44. 44 Struyf A , Hubert M , Rousseeuw P ( 1997 ) Clustering in an Object-Oriented Environment . Journal of Statistical Software 1 : 1 – 30 . 

  45. 45 Frank E , Hall M , Trigg L , Holmes G , Witten IH ( 2004 ) Data mining in bioinformatics using Weka . Bioinformatics 20 : 2479 – 2481 . 15073010 

관련 콘텐츠

오픈액세스(OA) 유형

GOLD

오픈액세스 학술지에 출판된 논문

저작권 관리 안내
섹션별 컨텐츠 바로가기

AI-Helper ※ AI-Helper는 오픈소스 모델을 사용합니다.

AI-Helper 아이콘
AI-Helper
안녕하세요, AI-Helper입니다. 좌측 "선택된 텍스트"에서 텍스트를 선택하여 요약, 번역, 용어설명을 실행하세요.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.

선택된 텍스트

맨위로