Spatial patterns of genome-wide expression profiles reflect anatomic and fiber connectivity architecture of healthy human brain

Human Brain Mapping

Volumn 35, Issue 8, 2014, Pages 4204-4218

  Goel, Pragya ^a   Kuceyeski, Amy ^b,c   Locastro, Eve ^b   Raj, Ashish ^b,c  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c MIND RESEARCH NETWORK   (United States)

Author keywords

Brain network; Gene similarity; Generalized discriminant analysis; Spatial clustering; White matter connectivity

Indexed keywords

ADH7 GENE; ADULT; ARTICLE; BAIAP2L2 GENE; BRAIN REGION; CAMK4 GENE; CBLN2 GENE; CD63 GENE; CDH12 GENE; CDH13 GENE; CONTROLLED STUDY; DIFFUSION TENSOR IMAGING; ENC1 GENE; FAM110C GENE; FTH1 GENE; GENE; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE MAPPING; GPR26 GENE; H1FX GENE; HGF GENE; HUMAN; HUMAN TISSUE; LGALS2 GENE; MBP GENE; MY018A GENE; NERVE CELL NETWORK; NERVE FIBER; NEUROANATOMY; NORMAL HUMAN; NTS GENE; PFDN2 GENE; PHIP GENE; PLP1 GENE; PRIORITY JOURNAL; SEMA4C GENE; SRGAP1 GENE; TF GENE; TPPP3 GENE; TRACTOGRAPHY; ANATOMY AND HISTOLOGY; BIOLOGICAL MODEL; BOOK; BRAIN; BRAIN MAPPING; GENETIC DATABASE; MICROARRAY ANALYSIS; NERVE TRACT; NUCLEAR MAGNETIC RESONANCE IMAGING; PHYSIOLOGY;

ATLASES AS TOPIC; BRAIN; BRAIN MAPPING; DATABASES, GENETIC; DIFFUSION TENSOR IMAGING; GENE EXPRESSION; HUMANS; MAGNETIC RESONANCE IMAGING; MICROARRAY ANALYSIS; MODELS, GENETIC; MODELS, NEUROLOGICAL; NEURAL PATHWAYS;

EID: 84903948402     PISSN: 10659471     EISSN: 10970193     Source Type: Journal    
DOI: 10.1002/hbm.22471     Document Type: Article

References (50)

1. Alemán-Gómez Y, Melie-García L, Valdés-Hernandez P (2006): IBASPM: Toolbox for automatic parcellation of brain structures. Available on CD-Rom in NeuroImage 31(Suppl 1). Available at http://www.thomaskoenig.ch/Lester/ibaspm.htm.
2. Alter O, Brown PO, Botstein D (2000): Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97:10101-10106.
3. Auffarth B (2007): Spectral graph clustering. Universitat de Barcelona, course report for Technicas Avanzadas de Aprendizaj, at Universitat Politecnica de Catalunya.
4. Bernard A, Lubbers LS, Tanis KQ, Luo R, Podtelezhnikov AA, Finney EM, McWhorter MME, Serikawa K, Lemon T, Morgan R, Copeland C, Smith K, Cullen V, Davis-Turak J, Lee CK, Sunkin SM, Loboda AP, Levine DM, Stone DJ, Hawrylycz MJ, Roberts CJ, Jones AR, Geschwind DH, Lein ES, (2012): Transcriptional architecture of the primate neocortex. Neuron 73:1083-1099.
5. Bohland JW, Bokil H, Pathak SD, Lee C-K, Ng L, Lau C, Kuan C, Hawrylycz M, Mitra PP (2010). Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy. Methods (San Diego, CA) 50:105-512.
6. Brodmann K (1909): Vergleichende Lokalisationslehre der Gro hirnrinde. Notes.
7. Brody JP, Williams BA, Wold BJ, Quake SR (2002): Significance and statistical errors in the analysis of DNA microarray data. Proc Natl Acad Sci USA 99:12975-12978.
8. Brown CS, Goodwin PC, Sorger PK (2001): Image metrics in the statistical analysis of DNA microarray data. Proc Natl Acad Sci USA 98:8944-8949.
9. Chen C-H, Panizzon MS, Eyler LT, Jernigan TL, Thompson W, Fennema-Notestine C, Jak AJ, Neale MC, Franz CE, Hamza S, Lyons MJ, Grant MD, Fischl B, Seidman LJ, Tsuang MT, Kremen WS, Dale AM (2011): Genetic influences on cortical regionalization in the human brain. Neuron 72:537-544.
10. Chen C-H, Gutierrez ED, Thompson W, Panizzon MS, Jernigan TL, Eyler LT, Fennema-Notestine C, Dale AM (2012): Hierarchical genetic organization of human cortical surface area. Science (New York, NY) 335:1634-1636.
11. Ebendal T (1992): Function and evolution in the NGF family and its receptors. J Neurosci Res 32:461-470.
12. Fisher R (1936): The use of multiple measurements in taxonomic problems. Ann Hum Genet 7:179-188.
13. Fodor IK (2002): A survey of dimension reduction techniques. LLNL Technical Report, UCRL-ID-148494:1-18.
14. French L, Pavlidis P (2011): Relationships between gene expression and brain wiring in the adult rodent brain. PLoS Comput Biol 7:e1001049.
15. French L, Patrick P, Tan C, Pavlidis P, Wolf L (2011): Large-scale analysis of gene expression and connectivity in the rodent brain: Insights through data integration. Gene Expression 5:1-11.
16. Friston KJ, Ashburner JT, Kiebel SJ, Nichols TE, Penny WD (2006): Statistical parametric mapping: the analysis of functional brain images. Friston, K 454-470.
17. Grange P, Mitra PP (2011): Statistical analysis of co-expression properties of sets of genes in the mouse brain arXiv preprint arXiv:1111.6200.
18. Greicius MD, Krasnow B, Reiss AL, Menon V (2003): Functional connectivity in the resting brain: A network analysis of the default mode hypothesis. Proc Natl Acad Sci USA 100:253-258.
19. Harrison BJ, Pujol J, López-Solà M, Hernández-Ribas R, Deus J, Ortiz H, Soriano-Mas C, Yusel M, Pantelis C, Cardoner N, (2008): Consistency and functional specialization in the default mode brain network. Proc Natl Acad Sci USA 105:9781-9786.
20. Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, Van de Lagemaat LN, et al. (2012): An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489:391-399.
21. Heerssen HM, Segal RA (2002): Location, location, location: A spatial view of neurotrophin signal transduction. Trends Neurosci 25:160-165.
22. Iturria-Medina Y, Canales-Rodriguez EJ, Aleman-Gomez Y, Sotero RC, Melie-Garcia L (2005): Bayesian formulation for fiber tracking. 11th Annual Meeting of the Organization for Human Brain Mapping (Toronto, Ontario, Canada). 26.
23. Iturria-Medina Y, Canales-Rodriguez EJ, Aleman-Gomez Y, Sotero RC, Melie-Garcia L (2008): Studying the human brain anatomical network via diffusion-weighted MRI and graph theory. NeuroImage 40:1064-1076.
24. Ivković M, Kuceyeski A, Raj A (2012): Statistics of weighted brain networks reveal hierarchical organization and gaussian degree distribution. PloS One 7:e35029.
25. Johnson MB, Kawasawa YI, Mason CE, Krsnik Z, Coppola G, Bogdanović D, Geschwind DH, Mane SM, State MW, Sestan N (2009): Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62:494-509.
26. Jones AR, Overly CC, Sunkin SM (2009): The allen brain atlas: 5 years and beyond. Nat Rev Neurosci 10:821-828.
27. Kasukawa T, Masumoto K-H, Nikaido I, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR (2011): Quantitative expression profile of distinct functional regions in the adult mouse brain. PloS One 6:e23228. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 3155528&tool=pmcentrez&rendertype=abstract.
28. Kaufman A, Dror G, Meilijson I, Ruppin E (2006): Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity. PLoS Comput Biol 2:e167.
29. Krzanowskit W (1995): Discriminant analysis with singular covariate matrices: Methods and applications to spectroscopic data. Appl Stat 44:101-115.
30. Kuceyeski A, Maruta J, Niogi SN, Ghajar J, Raj A (2011): The generation and validation of white matter connectivity importance maps. NeuroImage 58:109-121. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3144270&tool=pmcentrez&rendertype=abstract.
31. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, et al. (2007): Genome-wide atlas of gene expression in the adult mouse brain. Nature 445:168-176.
32. Lohof Ann M, Nancy Y, Mu-Ming P (1993): Potentiation of developing neuromuscular synapses by the neurotrophins NT-3 and BDNF. Nature 363:350-353.
33. Ng AM, Jordan YW, Weiss Y, (2002): On spectral clustering: analysis and an algorithm. Advances in Neural Information Processing Systems 14:849-856.
34. Rimol LM, Panizzon MS, Fennema-Notestine C, Eyler LT, Fischl B, Franz CE, Hagler DJ, Lyons MJ, Neale MC, Pacheco J, Perry ME, Schmitt JE, Grant MD, Seidman LJ, Thermenos HW, Tsuang MT, Eisen SA, Kremen WS, Dale AM (2010): Cortical thickness is influenced by regionally specific genetic factors. Biol Psychiatry 67:493-499.
35. Russo G, Zegar C, Giordano A (2003): Advantages and limitations of microarray technology in human cancer. Oncogene 22:6497-6507.
36. Schaeffer SE (2007): Graph clustering. Comp Sci Rev 1:27-64.
37. Schena M, Shalon D, Davis RW, Brown PO (1995): Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (New York, N.Y.) 270:467-470.
38. Scott EK, Luo L (2001): How do dendrites take their shape? Nat Neurosci 4:359-365.
39. Shalon D, Smith SJ, Brown PO (1996): A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6:639-645.
40. Singh S, Silakari S (2009): Generalized discriminant analysis algorithm for feature reduction in cyber. J Comp Sci 6:173-180.
41. Skaper SD (2012): The neurotrophin family of neurotrophic factors: an overview. Methods Mol Biol 846:1-12.
42. Smola AJ, Kondor R (2003): Kernels and regularization on graphs. Learning theory and kernel machines (Springer Berlin Heidelberg). 144-158.
43. Sunkin SM, Hohmann JG (2007): Insights from spatially mapped gene expression in the mouse brain. Hum Mol Genet 16:R209-R219.
44. Swanson LW (2000): What is the brain? Trends Neurosci 23:519-527.
45. Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, Mazoyer B, Joliot M (2002): Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. NeuroImage 15:273-289.
46. Wetmore C, Olson L (1995): Neuronal and nonneuronal expression of neurotrophins and their receptors in sensory and sympathetic ganglia suggest new intercellular trophic interactions. J Comp Neurol 353:143-159.
47. Wolf L, Goldberg C, Manor N, Sharan R, Ruppin E (2011): Gene expression in the rodent brain is associated with its regional connectivity. PLoS Comput Biol 7:e1002040.
48. Ye J (2005): Characterization of a family of algorithms for generalized discriminant analysis on undersampled problems. J Machine Learn Res 6:483-502.
49. Zapala MA, Hovatta I, Ellison JA, Wodicka L, Del Rio JA, Tennant R, Tynan W, Broide RS, Helton R, Stoveken BS, Winrow C, Lockhart DJ, Reilly JF, Young WG, Bloom FE, Lockhart DJ, Barlow C. (2005): Adult mouse brain gene expression patterns bear an embryologic imprint. Proc Natl Acad Sci USA 102:10357-10362.
50. Zilles K, Amunts K (2010): Centenary of Brodmann's map-Conception and fate. Nat Rev Neurosci 11:139-145.