An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome

Genome Biology

Volumn 5, Issue 1, 2003, Pages

  Hild, M ^a   Beckmann, B ^b   Haas, Sa ^c   Koch, B ^a   Solovyev, V ^d   Busold, C ^b   Fellenberg, K ^b   Boutros, M ^b   Vingron, M ^c   Sauer, F ^a,e   Hoheisel, Jd ^b   Paro, R ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^d SOFTBERRY INC   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Additional Data File; Additional Exon; Berkeley Drosophila Genome Project; Embryonic Stage; Gene Prediction

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; DNA MICROARRAY; DROSOPHILA MELANOGASTER; EVALUATION; GENE; GENE EXPRESSION PROFILING; GENETICS; GENOME; IN SITU HYBRIDIZATION; METHODOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; PREDICTION AND FORECASTING; PSEUDOGENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; STATISTICS;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENES, INSECT; GENOME; IN SITU HYBRIDIZATION; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREDICTIVE VALUE OF TESTS; PSEUDOGENES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE;

EID: 0742316351     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2003-5-1-r3     Document Type: Article

References (39)

1. Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP: A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell. 2001, 106: 413-415. DOI: 10.1016/S0092-8674(01)00467-6
2. Daly MJ: Estimating the human gene count. Cell. 2002, 109: 283-284. DOI: 10.1016/S0092-8674(02)00742-0
3. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al: The genome sequence of Drosophila melanogaster. Science. 2000, 287: 2185-2195. 10.1126/science.287.5461.2185. DOI: 10.1126/science.287.5461.2185
4. Karlin S, Bergman A, Gentles AJ: Genomics. Annotation of the Drosophila genome. Nature. 2001, 411: 259-260. 10.1038/35077152. DOI: 10.1038/35077152
5. Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, et al: Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet. 2001, 27: 337-340. 10.1038/85922. DOI: 10.1038/85922
6. Andrews J, Bouffard GG, Cheadle C, Lu J, Becker KG, Oliver B: Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res. 2000, 10: 2030-2043. 10.1101/gr.10.12.2030. DOI: 10.1101/gr.10.12.2030
7. Posey KL, Jones LB, Cerda R, Bajaj M, Huynh T, Hardin PE, Hardin SH: Survey of transcripts in the adult Drosophila brain. Genome Biol. 2001, 2: research0008.1-0008.16. 10.1186/gb-2001-2-3-research0008. DOI: 10.1186/gb-2001-2-3-research0008
8. Morin X, Daneman R, Zavortink M, Chia W: A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila. Proc Natl Acad Sci USA. 2001, 98: 15050-15055. 10.1073/pnas.261408198. DOI: 10.1073/pnas.261408198
9. Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, et al: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002, 3: research0083.1-0083.22. 10.1186/gb-2002-3-12-research0083. DOI: 10.1186/gb-2002-3-12-research0083
10. Reese MG, Kulp D, Tammana H, Haussler D: Genie - gene finding in Drosophila melanogaster. Genome Res. 2000, 10: 529-538. 10.1101/gr.10.4.529. DOI: 10.1101/gr.10.4.529
11. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997, 268: 78-94. 10.1006/jmbi.1997.0951. DOI: 10.1006/jmbi.1997.0951
12. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, et al: The genome sequence of the malaria mosquito Anopheles gambiae. Science. 2002, 298: 129-149. 10.1126/science.1076181. DOI: 10.1126/science.1076181
13. Drosophila pseudoobscura Genome Project. [http://www.hgsc.bcm.tmc.edu/projects/drosophila/]
14. Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, et al: Experimental annotation of the human genome using microarray technology. Nature. 2001, 409: 922-927. 10.1038/35057141. DOI: 10.1038/35057141
15. Rubin GM, Hong L, Brokstein P, Evans-Holm M, Frise E, Stapleton M, Harvey DA: A Drosophila complementary DNA resource. Science. 2000, 287: 2222-2224. 10.1126/science.287.5461.2222. DOI: 10.1126/science.287.5461.2222
16. Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000, 10: 516-522. 10.1101/gr.10.4.516. DOI: 10.1101/gr.10.4.516
17. Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M: GeneNest: automated generation and visualization of gene indices. Trends Genet. 2000, 16: 521-523. 10.1016/S0168-9525(00)02116-8. DOI: 10.1016/S0168-9525(00)02116-8
18. Haas SA, Hild M, Wright APH, Hain T, Talibi D, Vingron M: Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res. 2003, 31: 5576-5581. 10.1093/nar/gkg752. DOI: 10.1093/nar/gkg752
19. Fellenberg K, Hauser NC, Brors B, Neutzner A, Hoheisel JD, Vingron M: Correspondence analysis applied to microarray data. Proc Natl Acad Sci USA. 2001, 98: 10781-10786. 10.1073/pnas.181597298. DOI: 10.1073/pnas.181597298
20. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP: Gene expression during the life-cycle of Drosophila melanogaster. Science. 2002, 297: 2270-2275. 10.1126/science.1072152. DOI: 10.1126/science.1072152
21. White KP, Rifkin SA, Hurban P, Hogness DS: Microarray analysis of Drosophila development during metamorphosis. Science. 1999, 286: 2179-2184. 10.1126/science.286.5447.2179. DOI: 10.1126/science.286.5447.2179
22. Furlong EE, Andersen EC, Null B, White KP, Scott MP: Patterns of gene expression during Drosophila mesoderm development. Science. 2001, 293: 1629-1633. 10.1126/science.1062660. DOI: 10.1126/science.1062660
23. Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GB: Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002, 3: research0088.1-0088.14. 10.1186/gb-2002-3-12-research0088. DOI: 10.1186/gb-2002-3-12-research0088
24. The Heidelberg Prediction in situ patterns. [http://HDFlyArray.zmbh.uni-heidelberg.de/cgi-bin/insitu.pl]
25. Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, et al: The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 2002, 12: 1294-1300. 10.1101/gr.269102. DOI: 10.1101/gr.269102
26. Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, et al: C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet. 2003, 34: 35-41. 10.1038/ng1140. DOI: 10.1038/ng1140
27. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, et al: The generic genome browser: a building block for a model organism system database. Genome Res. 2002, 12: 1599-1610. 10.1101/gr.403602. DOI: 10.1101/gr.403602
28. The Heidelberg FlyArray GBrowser. [http://HDFlyArray.zmbh.uni-heidelberg.de/cgi-bin/gbrowse]
29. Jaillon O, Dossat C, Eckenberg R, Eiglmeier K, Segurens B, Aury JM, Roth CW, Scarpelli C, Brey PT, Weissenbach J, Wincker P: Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons. Genome Res. 2003, 13: 1595-1599. 10.1101/gr.922503. DOI: 10.1101/gr.922503
30. Exofish between the genome of Anopheles and the genome of Drosophila. [http://www.genoscope.cns.fr/externe/Fly/]
31. The FlyBase Consortium: The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 2003, 31: 172-175. 10.1093/nar/gkg094. DOI: 10.1093/nar/gkg094
32. Krause A, Haas SA, Coward E, Vingron M: SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. Nucleic Acids Res. 2002, 30: 299-300. 10.1093/nar/30.1.299. DOI: 10.1093/nar/30.1.299
33. Coward E, Haas SA, Vingron M: SpliceNest: visualizing gene structure and alternative splicing based on EST clusters. Trends Genet. 2002, 18: 53-55. 10.1016/S0168-9525(01)02525-2. DOI: 10.1016/S0168-9525(01)02525-2
34. Krause A, Stoye J, Vingron M: The SYSTERS protein sequence cluster set. Nucleic Acids Res. 2000, 28: 270-272. 10.1093/nar/28.1.270. DOI: 10.1093/nar/28.1.270
35. GenomePride. [http://pride.molgen.mpg.de]
36. Microarray data warehouse and analysis tools. [http://www.mchips.org]
37. Fellenberg K, Hauser NC, Brors B, Hoheisel JD, Vingron M: Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. Bioinformatics. 2002, 18: 423-433. 10.1093/bioinformatics/18.3.423. DOI: 10.1093/bioinformatics/18.3.423
38. Berkeley Drosophila Genome Project. [http://www.fruitfly.org/]
39. BDGP Download Miscellaneous Drosophila Sequences. [http://www.fruitfly.org/sequence/dlMisc.shtml]