Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis

Justen Andrews, Gerard G. Bouffard, Chris Cheadle, Jining Lü, Kevin G. Becker, Brian Oliver

Research output: Contribution to journalArticle

Abstract

Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized files. Additionally, >3% showed more than threefold overexpression at p

Original languageEnglish (US)
Pages (from-to)2030-2043
Number of pages14
JournalGenome Research
Volume10
Issue number12
DOIs
StatePublished - 2000
Externally publishedYes

Fingerprint

Genetic Association Studies
Microarray Analysis
Drosophila melanogaster
Testis
Expressed Sequence Tags
Genes
Drosophila
Genome
Molecular Sequence Annotation
Ovary
Complementary DNA
Messenger RNA
Population

ASJC Scopus subject areas

  • Genetics

Cite this

Andrews, J., Bouffard, G. G., Cheadle, C., Lü, J., Becker, K. G., & Oliver, B. (2000). Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Research, 10(12), 2030-2043. https://doi.org/10.1101/gr.10.12.2030

Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. / Andrews, Justen; Bouffard, Gerard G.; Cheadle, Chris; Lü, Jining; Becker, Kevin G.; Oliver, Brian.

In: Genome Research, Vol. 10, No. 12, 2000, p. 2030-2043.

Research output: Contribution to journalArticle

Andrews, J, Bouffard, GG, Cheadle, C, Lü, J, Becker, KG & Oliver, B 2000, 'Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis', Genome Research, vol. 10, no. 12, pp. 2030-2043. https://doi.org/10.1101/gr.10.12.2030
Andrews, Justen ; Bouffard, Gerard G. ; Cheadle, Chris ; Lü, Jining ; Becker, Kevin G. ; Oliver, Brian. / Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. In: Genome Research. 2000 ; Vol. 10, No. 12. pp. 2030-2043.
@article{9391ed5e0e3d4b5197c745a6c4cb4d3d,
title = "Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis",
abstract = "Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11{\%} correspond to named genes, and 33{\%} provide biological evidence for a predicted gene. A surprising 47{\%} fail to align with existing ESTs and 16{\%} with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80{\%} of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized files. Additionally, >3{\%} showed more than threefold overexpression at p",
author = "Justen Andrews and Bouffard, {Gerard G.} and Chris Cheadle and Jining L{\"u} and Becker, {Kevin G.} and Brian Oliver",
year = "2000",
doi = "10.1101/gr.10.12.2030",
language = "English (US)",
volume = "10",
pages = "2030--2043",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "12",

}

TY - JOUR

T1 - Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis

AU - Andrews, Justen

AU - Bouffard, Gerard G.

AU - Cheadle, Chris

AU - Lü, Jining

AU - Becker, Kevin G.

AU - Oliver, Brian

PY - 2000

Y1 - 2000

N2 - Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized files. Additionally, >3% showed more than threefold overexpression at p

AB - Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized files. Additionally, >3% showed more than threefold overexpression at p

UR - http://www.scopus.com/inward/record.url?scp=0034518604&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034518604&partnerID=8YFLogxK

U2 - 10.1101/gr.10.12.2030

DO - 10.1101/gr.10.12.2030

M3 - Article

VL - 10

SP - 2030

EP - 2043

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 12

ER -