MPI für molekulare Genetik / Department of Computational Molecular Biology |
|An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome|
|Authors:||Hild, M.; Beckmann, B.; Haas, Stefan. A.; Koch, B.; Solovyev, V.; Busold, C.; Fellenberg, K.; Boutros, M.; Vingron, Martin; Sauer, F.; Hoheisel, J. D.; Paro, R.|
|Date of Publication (YYYY-MM-DD):||2003-12-22|
|Title of Journal:||Genome Biology|
|Journal Abbrev.:||Genome Biol.|
|Issue / Number:||1|
|Copyright:||© 2003 Hild et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL|
|Review Status:||not specified|
|Abstract / Description:||Background
While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software.
Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly.
The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species.
|Free Keywords:||Genome studies, Model organisms, Bioinformatics, Development|
|Comment of the Author/Creator:||22 December 2003|
|External Publication Status:||published|
|Communicated by:||Martin Vingron|
|Affiliations:||MPI für molekulare Genetik|
|External Affiliations:||Max Planck Inst Mol Genet, D-14195 Berlin, Germany.; Univ Heidelberg, ZMBH, D-69120 Heidelberg, Germany.; Deutsches Krebsforschungszentrum, Div Funct Genome Anal, D-69120 Heidelberg, Germany.; Softberry Inc, Mt Kisko, NY 10549 USA.; Univ Calif Riverside, Dept Biochem, Riverside, CA 92521 USA.|
|Identifiers:||ISI:000187747000009 [ID No:1] |
ISSN:1465-6914 [ID No:2]
DOI:10.1186/gb-2003-5-1-r3 [ID No:3]
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