Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Crombach, Anton ^a   Cicin Sain, Damjan ^a   Wotton, Karl R ^a   Jaeger, Johannes ^a  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLOGMIA ALBIPUNCTATA; COLORIMETRY; COMPUTER AIDED DESIGN; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; CONTROLLED STUDY; DIPTERA; EMBRYO; EPISYRPHUS BALTEATUS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC DATABASE; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE SEGMENTATION; IN SITU HYBRIDIZATION; LABORATORY AUTOMATION; MEGASELIA ABDITA; MICROSCOPY; NONHUMAN; SPATIOTEMPORAL ANALYSIS; STRUCTURAL BIOINFORMATICS; WHOLE MOUNT IN SITU HYBRIDISATION; ANIMAL; ANIMAL EMBRYO; COMPUTER PROGRAM; DROSOPHILA; GENE; GENETICS; METABOLISM; METHODOLOGY;

TRANSCRIPTOME;

ANIMALS; DROSOPHILA; EMBRYO, NONMAMMALIAN; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENES, INSECT; IMAGE PROCESSING, COMPUTER-ASSISTED; IN SITU HYBRIDIZATION; SOFTWARE; TRANSCRIPTOME;

EID: 84874182270     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046658     Document Type: Article

References (37)

1. Megason SG, Fraser SE (2007) Imaging in Systems Biology. Cell 130: 784-95.
2. Kherlopian AR, Song T, Duan Q, Neimark MA, Po MJ, et al. (2008) A review of imaging techniques for systems biology. BMC Syst Biol 2: 74.
3. Surkova S, Myasnikova E, Janssens H, Kozlov KN, Samsonova AA, et al. (2008) Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. Fly 2: 1-9.
4. Shamir L, Delaney JD, Orlov JD, Eckley DM, Goldberg IG (2010) Pattern Recognition Software and Techniques for Biological Image Analysis. PLoS Comp Biol 6: e1000974.
5. Khairy K, Keller PJ (2011) Reconstructing Embryonic Development. Genesis 49: 488-513.
6. Akam M (1987) The molecular basis for metameric pattern in the Drosophila embryo. Development 101: 1-22.
7. Ingham PW (1988) The molecular genetics of embryonic pattern formation in Drosophila. Nature 335: 25-34.
8. St Johnston D, Nüsslein-Volhard C (1992) The origin of pattern and polarity in the Drosophila embryo. Cell 68: 201-19.
9. Furriols M, Casanova J (2003) In and out of Torso RTK signaling. EMBO J 22: 1947-52.
10. Jaeger J (2011) The Gap Gene Network. Cell Mol Life Sci 68: 243-74.
11. Jaeger J, Monk NAM (2010) Reverse Engineering of Gene Regulatory Networks. In: Lawrence ND, Girolami M, Rattray M, Sanguinetti G, editors. Learning and Inference in Computational Systems Biology. Cambridge, MA: MIT Press. pp 9-34.
12. Jaeger J, Crombach A (2012) Life's Attractors: Understanding Developmental Systems Through Reverse Engineering and In Silico Evolution. In: Soyer O, editor. Evolutionary Systems Biology. Berlin: Springer, p93-117.
13. Myasnikova E, Samsonova A, Kozlov KN, Samsonova M, Reinitz J (2001) Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics 17: 3-12.
14. Poustelnikova E, Pisarev A, Blagov M, Samsonova M, Reinitz J (2004) A database for management of gene expression data in situ. Bioinformatics 20: 2212-21.
15. Myasnikova E, Samsonova M, Kosman D, Reinitz J (2005) Removal of background signal from in situ data on the expression of segmentation genes in Drosophila. Dev Genes Evol 215: 320-6.
16. Janssens H, Kosman D, Vanario-Alonso CE, Jaeger J, Samsonova M, et al. (2005) A high-throughput method for quantifying gene expression data from early Drosophila embryos. Dev Genes Evol 215: 374-81.
17. Luengo Hendriks CL, Keranen SV, Fowlkes CC, Simirenko L, Weber GH, et al. (2006) Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol 7: R123.
18. Keranen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles DW, et al. (2006) Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics. Genome Biol 7: R124.
19. Fowlkes CC, Hendriks CL, Keranen SV, Weber GH, Rubel O, et al. (2008) A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133: 364-74.
20. Ay A, Fakhouri WD, Chiu C, Arnosti DN (2008) Image Processing and Analysis for Quantifying Gene Expression from Early Drosophila Embryos. Tissue Eng 14: 1517-26.
21. Surkova S, Kosman D, Kozlov K, Manu, Myasnikova E, et al. (2008) Characterization of the Drosophila segment determination morphome. Developmental Biology 313: 844-862.
22. Pisarev A, Poustelnikova E, Samsonova M, Reinitz J (2009) FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nuc Acids Res 37: D560-6.
23. Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 3: 0088.
24. Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A, et al. (2002) BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics 162: 2037-47.
25. Gurunathan R, Van Emden B, Panchanathan S, Kumar S (2004) Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. BMC Bioinformatics 5: 202.
26. Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 8: R145.
27. Peng H, Long F, Zhou J, Leung G, Eisen MB, et al. (2007) Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol 8 (Suppl I): S7.
28. Frise E, Hammonds AS, Celniker S (2010) Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol Syst Biol 6: 345.
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: 761-9.
30. Puniyani K, Faloutsos C, Xing EP (2010) SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images. Bioinformatics 26: i47-i56.
31. Crombach A, Wotton KR, Cicin-Sain D, Ashyraliyev M, Jaeger J (2012) Efficient reverse-engineering of a developmental gene regulatory network. PLoS Comp Biol 8: e1002589.
32. García Solache MA, Jaeger J, Akam M (2010) A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata. Dev Biol 344: 306-18.
33. Lemke S, Schmidt-Ott U (2009) Evidence for a composite anterior determinant in the hover fly Episyrphus balteatus (Syrphidae), a cyclorrhaphan fly with an anterodorsal serosa anlage. Development 136: 117-27.
34. Soille P (2003) Morphological Image Analysis: Principles and Applications. Berlin: Springer.
35. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-5.
36. Gonzalez RC, Woods RE (2002) Digital Image Processing. Upper Saddle River, NJ, U.S.A.: Prentice Hall.
37. Foley JD, van Dam A, Feiner SK, F HJ (1995) Computer Graphics: Principles and Practice. Reading, MA: Addison-Wesley.