Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images

Bioinformatics

Volumn 26, Issue 6, 2009, Pages 761-769

  Mace, Daniel L ^a   Varnado, Nicole ^a   Zhang, Weiping ^a   Frise, Erwin ^b   Ohler, Uwe ^a  

^a DUKE UNIVERSITY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951940746     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp658     Document Type: Article

References (41)

1. Bao, Z. et al. (2006) Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA, 103, 2707-2712.
2. Capovilla, M. et al. (1994) Direct regulation of decapentaplegic by Ultrabithorax and its role in Drosophila midgut morphogenesis. Cell, 76, 461-475.
3. Carpenter, A.E. et al. (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol., 7, R100.
4. Costa, I. et al. (2007) Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. BMC Bioinformatics, 8 (Suppl. 10), S3.
5. Damle, S.etal.(2006)Confocalquantificationofcis-regulatoryreportergeneexpression in living sea urchin. Dev. Biol., 299, 543-550.
6. Finklstein, R. and Perrimon, N. (1990) The orthodenticle gene is regulated by bicoid and torso and specifies Drosophila head development. Nature, 346, 485-488.
7. Fowlkes, C.C. et al. (2008)Aquantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell, 133, 364-374.
8. Gargesha, M. et al. (2005)A utomatic annotation techniques for gene expression images of the fruit fly embryo. In Visual Communications and Image Processing, Society of Photo-Optical Instrumentation Engineers, Bellingham, WA, pp. 576-583.
9. Harmon, C. et al. (2007) Comparative analysis of spatial patterns of gene expression in Drosophila melanogaster imaginal discs. Res. Comput. Mol. Biol., 4453, 533-547.
10. Hunt-Newbury, R. et al. (2007) High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol., 5, e237.
11. Janssens, H. et al. (2005) A high-throughput method for quantifying gene expression data from early Drosophila embryos. Dev. Genes Evol., 215, 374-381.
12. Kambadur, R. et al. (1998) Regulation of POU genes by castor and hunchback establishes layered compartments in the Drosophila CNS. Genes Dev., 12, 246-260.
13. Keller, P.J. et al. (2008) Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science, 322, 1065-1069.
14. Kennedy, J. and Eberhart, R. (1995) Particle swarm optimization. IEEE Intl Conf. Neural Netw., 4, 1942-1948.
15. Keranen, S.V.E. et al. (2006) 3D morphology and gene expression in the Drosophila blastoderm at cellular resolution ii: dynamics. Genome Biol., 7, R124.
16. Kraut, R. and Levine, M. (1991) Mutually repressive interactions between the gap genes giant and Kruppel define middle body regions of the Drosophila embryo. Development, 111, 611-621.
17. Kumar, S. et al. (2002) BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics, 162, 2037-2047.
18. Lee, J.-Y.Y. et al. (2006) Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl Acad. Sci. USA, 103, 6055-6060.
19. Leventon, M.E. et al. (2000) Statistical shape influence in geodesic active contours. IEEE Comput. Soc. Conf. Comput. Vis. Pattern Recogn., 1, 316-323.
20. Liu, Z. et al. (2007) Study of gene function based on spatial co-expression in a high- resolution mouse brain atlas. BMC Syst. Biol., 1, 1-19.
21. Mace, D.L. et al. (2006) Quantification of transcription factor expression from Arabidopsis images. Bioinformatics, 22, e323-e331.
22. Ma, Y. et al. (1998) Gene regulatory functions of Drosophila Fish-hook, a high mobility group domain Sox protein. Mech. Dev., 73, 169-182.
23. Megason, S.G. and Fraser, S.E. (2007) Imaging in systems biology. Cell, 130, 784-795.
24. Murray, J.I. et al. (2008)Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat. Methods, 5, 703-709.
25. Pan, J.-Y. et al. (2006) Automatic Mining of Fruit Fly Embryo Images.ACM, New York, NY, pp. 693-698.
26. Peng, H. and Myers, E.W. (2004) Comparing in situ mRNA expression patterns of Drosophila embryos. In Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB). Association for Computing Machinery, San Diego, CA, pp. 157-166.
27. Peng, H. et al. (2007) Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol., 8, 693-698.
28. Pirrotta, V. et al. (1995) Distinct parasegmental and imaginal enhancers and the establishment of the expression pattern of the Ubx gene. Genetics, 141, 1439-1450.
29. Rodriguez-Carranza, C.E. and Loew, M.H. (1998) Weighted and deterministic entropy measure for image registration using mutual information. In Medical Imaging 1998: Image Processing, Vol. 3338, 155-166.
30. Sanchez-Soriano, N. and Russell, S. (2000) Regulatory mutations of the Drosophila Sox gene Dichaete reveal new functions in embryonic brain and hindgut development. Dev. Biol., 220, 307-321.
31. Schroeder, M.D. et al. (2004) Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol., 2, e271.
32. Segal, E. et al. (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 535-540.
33. Steuer, R. et al. (2002) The mutual information detecting and evaluating dependencies between variables. Bioinformatics, 18, 231-240.
34. Theiler, J. and Prichard, D. (1996) Constrained-realization Monte-Carlo method for hypothesis testing. Physica D, 94, 221-235.
35. Tomancak, P. et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 3, research0088.1-research0088.14.
36. Tomancak, P. et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 8, R145.
37. Westerhuis, J.A. et al. (1998) Analysis of multiblock and hierarchical PCA and PLS models. J. Chemom., 12, 301-321.
38. Yeo, S. et al. (1995) On the functional overlap between two Drosophila POU homeo domain genes and the cell fate specification of a CNS neural precursor. Genes Dev., 9, 1223-1236.
39. Ye, J. et al. (2008) Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA. ACMTrans. Knowl. Dis. Data, 2, 1-21.
40. Zhou, J. and Peng, H. (2007) Automatic recognition and annotation of gene expression patterns of fly embryos. Bioinformatics, 23, 589-596.
41. Zitova, B. and Flusser, J. (2003) Image registration methods: a survey. Image Vis. Comput., 21, 977-1000.