Stability-driven nonnegative matrix factorization to interpret Spatial gene expression and build local gene networks

Proceedings of the National Academy of Sciences of the United States of America

Volumn 113, Issue 16, 2016, Pages 4290-4295

  Wu, Siqi ^a,b   Joseph, Antony ^a,b,c   Hammonds, Ann S ^b   Celniker, Susan E ^b   Yu, Bin ^a,d   Frise, Erwin ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c WalmartLabs   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Principal patterns; Sparse decomposition; Spatial gene expression; Spatially local networks; Stability selection

Indexed keywords

TRANSCRIPTION FACTOR;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CELL FATE; CONTROLLED STUDY; DROSOPHILA; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE MAPPING; GENE REGULATORY NETWORK; LASER SURGERY; LEARNING ALGORITHM; MOLECULAR GENETICS; NONHUMAN; NONNEGATIVE MATRIX FACTORIZATION; PRINCIPAL PATTERN; PRIORITY JOURNAL; SPATIAL GENE EXPRESSION; ANIMAL; BIOLOGICAL MODEL; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; GENETIC DATABASE; PHYSIOLOGY;

ANIMALS; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; MODELS, GENETIC;

EID: 84964344204     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1521171113     Document Type: Article

References (49)

1. Miller JA, et al. (2014) Transcriptional landscape of the prenatal human brain. Nature 508(7495):199-206.
2. Hawrylycz MJ, et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489(7416):391-399.
3. Almendro V, et al. (2014) Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Reports 6(3):514-527.
4. Almendro V, et al. (2014) Genetic and phenotypic diversity in breast tumor metastases. Cancer Res 74(5):1338-1348.
5. Bedard PL, Hansen AR, Ratain MJ, Siu LL (2013) Tumour heterogeneity in the clinic. Nature 501(7467):355-364.
6. Gerlinger M, et al. (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366(10):883-892.
7. de Bruin EC, et al. (2014) Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 346(6206):251-256.
8. Zhang J, et al. (2014) Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 346(6206):256-259.
9. Tomancak P, et al. (2002) Systematic determination of patterns of gene expression during drosophila embryogenesis. Genome Biol 3(12): research0088.1-88.14.
10. Yakoby N, et al. (2008) A combinatorial code for pattern formation in Drosophila oogenesis. Dev Cell 15(5):725-737.
11. Lécuyer E, et al. (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131(1):174-187.
12. Jenett A, et al. (2012) A GAL4-driver line resource for Drosophila neurobiology. Cell Reports 2(4):991-1001.
13. Jory A, et al. (2012) A survey of 6, 300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports 2(4):1014-1024.
14. Manning L, et al. (2012) A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS. Cell Reports 2(4):1002-1013.
15. Pollet N, et al. (2005) An atlas of differential gene expression during early Xenopus embryogenesis. Mech Dev 122(3):365-439.
16. Imai KS, Hino K, Yagi K, Satoh N, Satou Y (2004) Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: Towards a comprehensive understanding of gene networks. Development 131(16):4047-4058.
17. Smith CM, et al. (2007) The mouse gene expression database (gxd):2007 update. Nucleic Acids Res 35 (Database issue):D618-D623.
18. Richardson L, et al. (2009) Emage mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res 38 (Database issue):D703-D709.
19. Lein ES, et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445(7124):168-176.
20. Tomancak P, et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 8(7):R145.
21. Hammonds AS, et al. (2013) Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biol 14(12):R140.
22. Peng H, et al. (2007) Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol 8(Suppl 1):S7.
23. Zhou J, Peng H (2007) Automatic recognition and annotation of gene expression patterns of fly embryos. Bioinformatics 23(5):589-596.
24. Pruteanu-Malinici I, Mace DL, Ohler U (2011) Automatic annotation of spatial expression patterns via sparse Bayesian factor models. PLOS Comput Biol 7(7):e1002098.
25. Pruteanu-Malinici I, Majoros WH, Ohler U (2013) Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields. Bioinformatics 29(13):i27-i35.
26. Yuan L, et al. (2014) Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. Bioinformatics 30(2):266-273.
27. Frise E, Hammonds AS, Celniker SE (2010) Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol Syst Biol 6:345.
28. Puniyani K, Faloutsos C, Xing EP (2010) SPEX2: Automated concise extraction of spatial gene expression patterns from Fly embryo ISH images. Bioinformatics 26(12):i47-i56.
29. Mace DL, Varnado N, Zhang W, Frise E, Ohler U (2010) Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. Bioinformatics 26(6):761-769.
30. Puniyani K, Xing EP (2013) GINI: From ISH images to gene interaction networks. PLOS Comput Biol 9(10):e1003227.
31. Adryan B, Teichmann SA (2010) The developmental expression dynamics of Drosophila melanogaster transcription factors. Genome Biol 11(4):R40.
32. Schulz C, Tautz D (1994) Autonomous concentration-dependent activation and repression of Krüppel by hunchback in the Drosophila embryo. Development 120(10):3043-3049.
33. Kvon EZ, et al. (2014) Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512(7512):91-95.
34. Stanojevic D, Small S, Levine M (1991) Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254(5036):1385-1387.
35. Lohs-Schardin M, Cremer C, Nüsslein-Volhard C (1979) A fate map for the larval epidermis of Drosophila melanogaster: Localized cuticle defects following irradiation of the blastoderm with an ultraviolet laser microbeam. Dev Biol 73(2):239-255.
36. Hartenstein V (1993) Atlas of Drosophila Development (Cold Spring Harbor Laboratory Press, Plainview, NY).
37. Lee DD, Seung HS (1999) Learning the parts of objects by non-negative matrix factorization. Nature 401(6755):788-791.
38. Amari S, Cichocki A, Yang H (1996) A new learning algorithm for blind signal separation. Advances in Neural Information Processing Systems (MIT Press, Cambridge, MA), pp 757-763.
39. Hyvärinen A (1999) Fast and robust fixed-point algorithms for independent component analysis. IEEE Trans Neural Networks 10(3):626-634.
40. Nüsslein-Volhard C, Wieschaus E (1980) Mutations affecting segment number and polarity in Drosophila. Nature 287(5785):795-801.
41. Tibshirani R (1996) Regression shrinkage and selection via the lasso. J Royal Statist Soc B 58(1):267-288.
42. Ashraf SI, Hu X, Roote J, Ip YT (1999) The mesoderm determinant snail collaborates with related zinc-finger proteins to control Drosophila neurogenesis. EMBO J 18(22):6426-6438.
43. Wang YX, Huang H (2014) Review on statistical methods for gene network reconstruction using expression data. J Theor Biol 362:53-61.
44. Jaeger J (2011) The gap gene network. Cell Mol Life Sci 68(2):243-274.
45. Nüsslein-Volhard C, Kluding H, Jürgens G (1985) Genes affecting the segmental subdivision of the Drosophila embryo. Cold Spring Harb Symp Quant Biol 50:145-154.
46. Brunet JP, Tamayo P, Golub TR, Mesirov JP (2004) Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci USA 101(12):4164-4169.
47. Tan VY, Févotte C (2013) Automatic relevance determination in nonnegative matrix factorization with the β-divergence. IEEE Trans Pattern Anal Mach Intell 35(7):1592-1605.
48. Sun M, Zhang X (2015) A stable approach for model order selection in nonnegative matrix factorization. Pattern Recognit Lett 54:97-102.
49. Margolis JS, et al. (1995) Posterior stripe expression of hunchback is driven from two promoters by a common enhancer element. Development 121(9):3067-3077.