Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings

Methods

Volumn 73, Issue , 2015, Pages 79-89

  Mahfouz, Ahmed ^a,b   van de Giessen, Martijn ^a,b   van der Maaten, Laurens ^a,b   Huisman, Sjoerd ^a,b   Reinders, Marcel ^b   Hawrylycz, Michael J ^c   Lelieveldt, Boudewijn P F ^a,b  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^c ALLEN INSTITUTE FOR BRAIN SCIENCE   (United States)

Author keywords

Allen brain atlas; Brain transcriptome structure; Dimensionality reduction; Spatial mapped gene expression; Stochastic neighbor embedding

Indexed keywords

TRANSCRIPTOME;

ADULT; ANATOMICAL CONCEPTS; ANIMAL TISSUE; ARTICLE; ASTROCYTE; BARNES HUT STOCHASTIC NEIGHBOR EMBEDDING; BRAIN; BRAIN MAPPING; BRAIN REGION; BRAIN SLICE; CLINICAL ARTICLE; CONTROLLED STUDY; EMBEDDING; FEMALE; GENE EXPRESSION; HEMISPHERE; HIPPOCAMPUS; HUMAN; HUMAN TISSUE; IN SITU HYBRIDIZATION; MALE; MIDDLE AGED; MOUSE; NERVE CELL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; OLIGODENDROGLIA; PRIORITY JOURNAL; YOUNG ADULT; ANATOMY AND HISTOLOGY; ANIMAL; BOOK; C57BL MOUSE; GENE EXPRESSION REGULATION; GENETICS; NONLINEAR SYSTEM; PHYSIOLOGY; PROCEDURES;

MAMMALIA;

ADULT; ANIMALS; ATLASES AS TOPIC; BRAIN; BRAIN MAPPING; FEMALE; GENE EXPRESSION REGULATION; HUMANS; MALE; MICE; MICE, INBRED C57BL; MIDDLE AGED; NONLINEAR DYNAMICS; TRANSCRIPTOME; YOUNG ADULT;

EID: 84922741323     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2014.10.004     Document Type: Article

References (31)

1. Swanson L.W. Brain Architecture: Understanding the Basic Plan 2011, Oxford University Press, New York. second ed.
2. Hawrylycz M., Ng L., Page D., Morris J., Lau C., Faber S., et al. Neural Netw. 2011, 24:933-942. 10.1016/j.neunet.2011.06.012.
3. Ng L., Bernard A., Lau C., Overly C.C., Dong H.-W., Kuan C., et al. Nat. Neurosci. 2009, 12:356-362. 10.1038/nn.2281.
4. Richardson L., Venkataraman S., Stevenson P., Yang Y., Moss J., Graham L., et al. Nucleic Acids Res. 2014, 42. 10.1093/nar/gkt1155.
5. The Gene Expression Nervous System Atlas (GENSAT) Project, NINDS Contracts N01NS02331 & HHSN271200723701C to The Rockefeller University, New York, NY, 2003.
6. Lein E.S., Hawrylycz M.J., Ao N., Ayres M., Bensinger A., Bernard A., et al. Nature 2007, 445:168-176. 10.1038/nature05453.
7. Hawrylycz M.J., Lein E.S., Guillozet-Bongaarts A.L., Shen E.H., Ng L., Miller J.A., et al. Nature 2012, 489:391-399. 10.1038/nature11405.
8. Bohland J.W., Bokil H., Pathak S.D., Lee C.-K., Ng L., Lau C., et al. Methods 2010, 50:105-112. 10.1016/j.ymeth.2009.09.001.
9. Ko Y., Ament S.A., Eddy J.A., Caballero J., Earls J.C., Hood L., et al. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:3095-3100. 10.1073/pnas.1222897110.
10. Williams C.K.I. Mach. Learn. 2002, 46:11-19. 10.1023/A:1012485807823.
11. Venna J., Peltonen J., Nybo K., Aidos H., Kaski S. J. Mach. Learn. Res. 2010, 11:451-490.
12. Van Der Maaten L., Hinton G. J. Mach. Learn. Res. 2008, 9:2579-2605. 10.1007/s10479-011-0841-3.
13. Tenenbaum J.B., de Silva V., Langford J.C. Science 2000, 290:2319-2323. 10.1126/science.290.5500.2319.
14. Lunga D., Prasad S., Crawford M.M., Ersoy O. IEEE Signal Process. Mag. 2014, 31:55-66. 10.1109/MSP.2013.2279894.
15. Shekhar K., Brodin P., Davis M.M., Chakraborty A.K. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:202-207. 10.1073/pnas.1321405111.
16. Ji S. BMC Bioinformatics 2013, 14:222. 10.1186/1471-2105-14-222.
17. Fonville J.M., Carter C.L., Pizarro L., Steven R.T., Palmer A.D., Griffiths R.L., et al. Anal. Chem. 2013, 85:1415-1423. 10.1021/ac302330a.
18. Allen Institute for Brain Science. Allen Mouse Brain Atlas [Internet], (2014). Available from: http://mouse.brain-map.org/.
19. Ng L., Pathak S.D., Kuan C., Lau C., Dong H., Sodt A., et al. IEEE/ACM Trans. Comput. Biol. Bioinform. 2007, 4:382-393. 10.1109/tcbb.2007.1035.
20. Lau C., Ng L., Thompson C., Pathak S., Kuan L., Jones A., et al. BMC Bioinformatics 2008, 9:153. 10.1186/1471-2105-9-153.
21. Allen Institute for Brain Science. Allen Human Brain Atlas [Internet], (2014). Available from: http://human.brain-map.org/.
22. Allen Human Brain Atlas Technical White Paper: Microarray Data Normalization, 2013.
23. Cahoy J., Emery B., Kaushal A., Foo L., Zamanian J., Christopherson K., et al. J. Neurosci. 2008, 28:264-278. 10.1523/JNEUROSCI.4178-07.2008.
24. Cox T.F., Cox M.A.A. Multidimensional Scaling 1994, Chapman & Hall.
25. Sharma G. Digital Color Imaging Handbook 2003, CRC Press. 1.7.2 ed.
26. Holmes C.J., Hoge R., Collins L., Woods R., Toga A.W., Evans A.C. J. Comput. Assist. Tomogr. 1998, 22(2):324-333. 10.1097/00004728-199803000-00032.
27. Webb A.R. Statistical Pattern Recognition 2002, John Wiley and Sons Ltd. second ed.
28. van der Maaten L.J.P. J. Mach. Learn. Res. 2014.
29. Barnes J., Hut P. Nature 1986, 324:446-449. 10.1038/324446a0.
30. Greengard L., Rokhlin V. J. Comput. Phys. 1987, 73:325-348. 10.1016/0021-9991(87)90140-9.
31. M. Vladymyrov, M. Carreira-Perpinan, Linear-time training of nonlinear low-dimensional embeddings, in: 17th Int. Conf. Artif. Intell. Stat. (AISTATS 2014), 2014, pp. 968-977.