Single-feature polymorphism discovery in the barley transcriptome

Nils Rostoks; Justin O Borevitz; Peter E Hedley; Joanne Russell; Sharon Mudie; Jenny Morris; Linda Cardle; David F Marshall; Robbie Waugh

doi:10.1186/gb-2005-6-6-r54

Single-feature polymorphism discovery in the barley transcriptome

Nils Rostoks, Justin O Borevitz, Peter E Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David F Marshall, Robbie Waugh

Research output: Contribution to journal › Article › peer-review

135 Citations (Scopus)

Abstract

A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.

Original language	English
Article number	R54
Journal	Genome Biology
Volume	6
Issue number	6
DOIs	https://doi.org/10.1186/gb-2005-6-6-r54
Publication status	Print publication - May 2005
Externally published	Yes

Keywords

Animal Genetics and Genomics
Bioinformatics
Evolutionary Biology
Golden Promise
Human Genetics
International Collaborative Project
Microbial Genetics and Genomics
Mutation Surveyor Software
Oregon Wolfe Barley
Plant Genetics & Genomics
Sequence Polymorphism

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10.1186/gb-2005-6-6-r54

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title = "Single-feature polymorphism discovery in the barley transcriptome",

abstract = "A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67\% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.",

keywords = "Animal Genetics and Genomics, Bioinformatics, Evolutionary Biology, Golden Promise, Human Genetics, International Collaborative Project, Microbial Genetics and Genomics, Mutation Surveyor Software, Oregon Wolfe Barley, Plant Genetics \& Genomics, Sequence Polymorphism",

author = "Nils Rostoks and Borevitz, \{Justin O\} and Hedley, \{Peter E\} and Joanne Russell and Sharon Mudie and Jenny Morris and Linda Cardle and Marshall, \{David F\} and Robbie Waugh",

year = "2005",

month = may,

doi = "10.1186/gb-2005-6-6-r54",

language = "English",

volume = "6",

journal = "Genome Biology",

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publisher = "BioMed Central",

number = "6",

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T1 - Single-feature polymorphism discovery in the barley transcriptome

AU - Rostoks, Nils

AU - Borevitz, Justin O

AU - Hedley, Peter E

AU - Russell, Joanne

AU - Mudie, Sharon

AU - Morris, Jenny

AU - Cardle, Linda

AU - Marshall, David F

AU - Waugh, Robbie

PY - 2005/5

Y1 - 2005/5

N2 - A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.

AB - A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.

KW - Animal Genetics and Genomics

KW - Bioinformatics

KW - Evolutionary Biology

KW - Golden Promise

KW - Human Genetics

KW - International Collaborative Project

KW - Microbial Genetics and Genomics

KW - Mutation Surveyor Software

KW - Oregon Wolfe Barley

KW - Plant Genetics & Genomics

KW - Sequence Polymorphism

UR - http://www.mendeley.com/research/singlefeature-polymorphism-discovery-barley-transcriptome

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DO - 10.1186/gb-2005-6-6-r54

M3 - Article

SN - 1474-7596

VL - 6

JO - Genome Biology

JF - Genome Biology

IS - 6

M1 - R54

ER -

Single-feature polymorphism discovery in the barley transcriptome

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Keywords

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