BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development

Genetics

Volumn 162, Issue 4, 2002, Pages 2037-2047

  Kumar, Sudhir ^a,b   Jayaraman, Karthik ^c   Panchanathan, Sethuraman ^a,c   Gurunathan, Rajalakshmi ^a,c   Marti Subirana, Ana ^d   Newfeld, Stuart J ^b  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c Arizona State University   (United States)

^d Phoenix College   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; CALCULATION; COMPUTER PROGRAM; DEVELOPMENTAL BIOLOGY; DEVICE INFECTION; DROSOPHILA MELANOGASTER; EMBRYO; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE PROBE; GENETIC DATABASE; GENOTYPE; IMAGING SYSTEM; INSECT DEVELOPMENT; NONHUMAN; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; DNA, COMPLEMENTARY; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, INSECT; PHENOTYPE; RNA; SOFTWARE;

ARACHNIDA; DROSOPHILA MELANOGASTER; EUKARYOTA; HEXAPODA; INSECTA; MELANOGASTER;

EID: 12244265472     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (66)

1. ADAMS, R., and L. BISCHOF, 1994 Seeded region growing. IEEE Transactions on Patterns Analysis and Mach. Intell. 16: 641-647.
2. ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS and D.J. LIPMAN, 1990 Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. ARNOSTI, D. N., S. GRAY, S. BAROLO, J. ZHOU and M. LEVINE, 1996 The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo. EMBO J. 15: 3659-3666.
4. ASHE, H. L., and M. LEVINE, 1999 Local inhibition and long-range enhancement of Dpp signal transduction by Sog. Nature 398: 427-431.
5. CARROLL, S. B., J. K. GRENIER and S. D. WEATHERBEE, 2000 From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Blackwell Science, Oxford.
6. CASARES, F., and E. SANCHEZ-HERRERO, 1995 Regulation of the infraabdominal regions of the bithorax complex of Drosophila by gap genes. Development 121: 1855-1866.
7. CASTLEMAN, K. R., 1996 Digital Image Processing. Prentice-Hall, Englewood Cliffs, NJ.
8. COSTA, L. F., and R. M. CESAR, 2000 Shape Analysis and Classification: Theory and Practice. CRC Press, Cleveland.
9. DAVIDSON, E., 2000 Genomic Regulatory Systems: Development and Evolution. Academic Press, New York.
10. FLORES-SAAIB, R. D., S. JIA and A. J. COUREY, 2001 Activation and repression by the C-terminal domain of Dorsal. Development 128: 1869-1879.
11. FUJIOKA, M., J. B. JAYNES and T. GOTO, 1995 Early even-skipped stripes act as morphogenetic gradients at the single cell level to establish engrailed expression. Development 121: 4371-4382.
12. GAUL, U., and H. JACKLE, 1987 Pole region-dependent repression of the Drosophila gap gene Krüppel by maternal gene products. Cell 51: 549-555.
13. GAUL, U., and H. JACKLE, 1990 Role of gap genes in early Drosophila development, pp. 239-275 in Genetic Regulatory Hierarchies in Development, edited by T. R. F. WRIGHT. Academic Press, San Diego.
14. GIESELER, K., E. WILDER, M. C. MARIOL, M. BURATOVITCH, H. BERENCER et al., 2001 DWnt4 and wingless elicit similar cellular responses during imaginal development. Dev. Biol. 232: 339-350.
15. GOLDSTEIN, L. S. B., and E. A. FYRBERG (Editors), 1994 Drosophila melanogaster: Practical Uses in Cell and Molecular Biology. Academic Press, San Diego.
16. GOLDSTEIN, R. E., G. JIMENEZ, O. COOK, D. GUR and Z. PAROUSH, 1999 Huckebein repressor activity in Drosophila terminal patterning is mediated by Groucho. Development 126: 3747-3755.
17. GONZALEZ, R., and R. WOODS, 1993 Digital Image Processing. Addison-Wesley, Reading, MA.
18. GROSSNIKLAUS, U., K. M. CADIGAN and W.J. GEHRING, 1994 Three maternal coordinate systems cooperate in the patterning of the Drosophila head. Development 120: 3155-3171.
19. GUTJAHR, T., E. FREI and M. NOLL, 1993 Complex regulation of early paired expression: initial activation by gap genes and pattern modulation by pair-rule genes. Development 117: 609-623.
20. HARTMANN, C., H. TAUBERT, H. JACKLE and M. J. PANKRATZ, 1994 A two-step mode of stripe formation in the Drosophila blastoderm requires interactions among primary pair rule genes. Mech. Dev. 45: 3-13.
21. HULSKAMP, M., and D. TAUTZ, 1991 Gap genes and gradients - the logic behind the gaps. Bioessays 13: 261-268.
22. HULSKAMP, M., C. PFEIFLF and D. TAUTZ, 1990 A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel and knirps in the early Drosophila embryo. Nature 346: 577-580.
23. HULSKAMP, M., W. LUKOWITZ, A. BEERMANN, G. GLASER and D. TAUTZ, 1994 Differential regulation of target genes by different alleles of the segmentation gene hunchback in Drosophila. Genetics 138: 125-134.
24. JANODY, F., J. REISCHL and N. DOSTATNI, 2000 Persistence of Hunchback in the terminal region of the Drosophila blastoderm embryo impairs anterior development. Development 127: 1573-1582.
25. JAZWINSKA, A., N. KIROV, E. WIESCHAUS, S. ROTH and C. RUSHLOW, 1999a The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation. Cell 96: 563-573.
26. JAZWINSKA, A., C. RUSHLOW and S. ROTH, 1999b The role of brinker in mediating the graded response to Dpp in early Drosophila embryo. Development 126: 3323-3334.
27. JIN, S., S. MARINKE, W. S. JOO, J. R. WORTMAN, N. MIRKOVIC et al., 2000 Identification and characterization of a p53 homologous in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 97: 7301-7306.
28. KANIA, M. A., A. S. BONNER, J. B. DUFFY and J. P. GERGEN, 1990 The Drosophila segmentation gene runt encodes a novel nuclear regulatory protein that is also expressed in the developing nervous system. Genes Dev. 4: 1701-1713.
29. KLINGLER, M., J. SOONG, B. BUTLER and J. P. GERGEN, 1996 Disperse versus compact elements for the regulation of runt stripes in Drosophila. Dev. Biol. 177: 73-84.
30. KOBAYASHI, M., R. E. GOLDSTEIN, M. FUJIOKA, Z. PAROUSH and J. B. JAYNES, 2001 Groucho augments the repression of multiple Even skipped target genes in establishing parasegment boundaries. Development 128: 1805-1815.
31. KOSMAN, D., and S. SMALL, 1997 Concentration-dependent patterning by an ectopic expression domain of the Drosophila gap gene knirps. Development 124: 1343-1354.
32. LARDELLI, M., and D. ISH-HOROWICZ, 1993 Drosophila hairy pairrule gene regulates embryonic patterning outside its apparent stripe domains. Development 118: 255-266.
33. LA ROSEE-BORGGREVE, A., T. HADER, D. WAINWRIGHT, F. SAUER and H. JACKLE, 1999 hairy stripe 7 element mediates activation and repression in response to different domains and levels of Krüppel in the Drosophila embryo. Mech. Dev. 89: 133-140.
34. LAWRENCE, P. A., and P. JOHNSTON, 1989 Analysis of function of the pair-rule genes hairy, even-skipped and fushi tarazu in mosaic Drosophila embryos. Development 107: 847-853.
35. LAWRENCE, P. A., and L. PICK, 1998 How does the fushi tarazu gene activate engrailed in the Drosophila embryo? Dev. Genet. 23: 28-34.
36. LIE, W.-N., 1995 Automatic target segmentation by locally adaptive image thresholding. IEEE Transactions on Image Processing 4: 1036-1041.
37. MAcDONALD, P. M., 1990 bicoid MRNA localization signal: phyllogenetic conservation of function and RNA secondary structure. Development 110: 161-171.
38. MARGOLIS, J. S., M. L. BOROWSKY, E. STEINGRIMSSON, C. W. SHIM, J. A. LENGYEL, et al., 1995 Posterior stripe expression of hunchback is driven from two promoters by a common enhancer element. Development 121: 3067-3077.
39. NASIADKA, A., A. GRILL and H. M. KRAUSE, 2000 Mechanisms regulating target gene selection by the homeodomain-containing protein Fushi tarazu. Development 127: 2965-2976.
40. NIBU, Y., and M. S. LEVINE, 2001 CtBP-dependent activities of the short-range Giant repressor in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 98: 6204-6208.
41. NIBU, Y., H. ZHANG, E. BAJOR, S. BAROLO, S. SMALL et al., 1998 dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo. EMBO J. 17: 7009-7020.
42. NIESSING, D., N. DOSTATNI, H. JACKLE and R. RIVERA-POMAR, 1999 Sequence interval within the PEST motif of Bicoid is important for translational repression of caudal mRNA in the anterior region of the Drosophila embryo. EMBO J. 18: 1966-1973.
43. PANKRATZ, M. J., and H. JACKLE, 1990 Making stripes in the Drosophila embryo. Trends Genet. 6: 287-292.
44. PANKATZ, M. J., M. HOCH, E. SEIFERT and H. JACKLE, 1989 Krüppel requirement for knirps enhancement reflects overlapping gap gene activities in the Drosophila embryo. Nature 341: 337-340.
45. PANKRATZ, M. J., E. SEIFERT, N. GERWIN, B. BILLI, U. NAUBER et al., 1990 Gradients of Krüppel and knirps gene products direct pair-rule gene stripe patterning in the posterior region of the Drosophila embryo. Cell 61: 309-317.
46. PELEGRI, F., and R. LEHMANN, 1994 A role of polycomb group genes in the regulation of gap gene expression in Drosophila. Genetics 136: 1341-1353.
47. PIGNONI, F., E. STEINGRIMSSON and J. A. LENGYEL, 1992 bicoid and the terminal system activate tailless expression in the early Drosophila embryo. Development 115: 239-251.
48. RAY, R. P., K. ARORA, C. NUSSLEIN-VOLHARD and W. M. GELBART, 1991 The control of cell fate along the dorsal-ventral axis of the Drosophila embryo. Development 113: 35-54.
49. RIDDIHOUGH, G., and D. ISH-HOROWICZ, 1991 Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes. Genes Dev. 5: 840-854.
50. RIVERA-POMAR, R., X. Lu, N. PERRIMON, H. TAUBERT and H. JACKLE, 1995 Activation of posterior gap gene expression in the Drosophila blastoderm. Nature 376: 253-256.
51. ROTHE, M., E. A. WIMMER, M. J. PANKRATZ, M. GONZALEZ-GAITAN and H. JACKLE, 1994 Identical transacting factor requirement for knirps and knirps-related gene expression in the anterior but not in the posterior region of the Drosophila embryo. Mech. Dev. 46: 169-181.
52. ROUGVIE, A. E., 2001 Control of developmental timing in animals. Nat. Rev. Genet. 2: 690-701.
53. SCHULZ, C., and D. TAUTZ, 1994 Autonomous concentration-dependent activation and repression of Krüppel by hunchback in the Drosophila embryo. Development 120: 3043-3049.
54. SCHULZ, C., and D. TAUTZ, 1995 Zygotic caudal regulation by hunchback and its role in abdominal segment formation of the Drosophila embryo. Development 121: 1023-1028.
55. SOMMER, R., and D. TAUTZ, 1991 Segmentation gene expression in the housefly Musca domestica. Development 113: 419-430.
56. STEINGRIMSSON, E., F. PIGNONI, G. J. LIAW and J. A. LENGYEL, 1991 Dual role of the Drosophila pattern gene tailless in embryonic termini. Science 254: 418-421.
57. TAKAESU, N. T., A. N. JOHNSON, O. H. SULTANI and S. J. NEWFELD, 2002 Combinatorial signaling by an unconventional Wg pathway and the Dpp pathway requires Nejire (CBP/p300) to regulate dpp expression in posterior tracheal branches. Dev. Biol. 247: 225-236.
58. TAUTZ, D., 1988 Regulation of the Drosophila segmentation gene hunchback by two maternal morphogenetic centres. Nature 332: 281-284.
59. Toy, J., J.-M. YANG, G. S. LEPPERT and O. H. SUNDIN, 1998 The Optx2 homeobox is expressed in early precursors of the eye and activates retina-specific genes. Proc. Natl. Acad. Sci. USA 95: 10643-10648.
60. TSAI, C., and J. P. GERGEN, 1994 Gap gene properties of the pairrule gene runt during Drosophila segmentation. Development 120: 1671-1683.
61. TSAI, C. C., S. G. KRAMER and J. P. GERGEN, 1998 Pair-rule gene runt restricts orthodenticle expression to the presumptive head of the Drosophila embryo. Dev. Genet. 23: 35-44.
62. VINCENT, A., J. T. BLANKENSHIP and E. WIESCHAUS, 1997 Integration of the head and trunk segmentation systems controls cephalic furrow formation in Drosophila. Development 124: 3747-3754.
63. WIMMER, E. A., A. CARLETON, P. HARJES, T. TURNER and C. DESPLAN, 2000 Bicoid-independent formation of thoracic segments in Drosophila. Science 287: 2476-2479.
64. Wu, X., R. VAKANI and S. SMALL, 1998 Two distinct mechanisms for differential positioning of gene expression borders involving the Drosophila gap protein giant. Development 125: 3765-3774.
65. Yu, Y., and L. PICK, 1995 Non-periodic cues generate seven ftz stripes in the Drosophila embryo. Mech. Dev. 50: 163-175.
66. ZHANG, H., and M. LEVINE, 1999 Groucho and dCtBP mediate separate pathways of transcriptional repression in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 96: 535-540.