A two-stage binomial test approach of gene identification in oligonucleotide arrays.

A two-stage binomial test approach of gene identification in oligonucleotide arrays. Research Abstract Details 

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A two-stage binomial test approach of gene identification in oligonucleotide arrays. Abstract Text:

Dung-Tsa Chen,James J Chen,Gary Cheng,Sue-Hwa Lin,Seng-Jaw Soong,

Most statistical approaches summarize the probe-level expression data into gene-level measures, which then are used for downstream statistical analyses. However, there are some limitations in using the gene level data for analysis, such as nonhomogeneous probe effects and the interaction effect (e.g., alternative splicing). In this paper, we consider a two-stage binomial test with a weighted probe rank approach to determine differentially expressed genes. Using a series of benchmark gene array datasets, we show the two-stage binomial test approach yielded a higher positive predictivity and a higher sensitivity than the conventional RMA, GCRMA, Dchip, and ANOVA approaches. In data application, the two-stage binomial test identified a subset of genes strongly related to cell proliferation in the prolactin study, and a subset of genes associated with lymph node metastasis in the breast cancer dataset. In addition, by exploring the proportion of probes with expression changes and the probe expression plot, the two-stage binomial test helped detect an alternative splicing form of the prolactin gene in the prolactin study. In the breast cancer dataset, the approach also identified one potential alternative splicing gene.

A two-stage binomial test approach of gene identification in oligonucleotide arrays. Publishing Authors By Initials

DT Chen,JJ Chen,G Cheng,SH Lin,SJ Soong,

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MEDLINE DATE:

A two-stage binomial test approach of gene identification in oligonucleotide arrays. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Journal of biopharmaceutical statistics

VOLUME: 17

Page Numbers: 903-18

Journal Abbreviation:

ISSN: 1054-3406

DAY: 3

MONTH: 12

YEAR: 2007

A two-stage binomial test approach of gene identification in oligonucleotide arrays. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9200436

A two-stage binomial test approach of gene identification in oligonucleotide arrays. Keywords Mesh Terms:

KEYWORDS: Reverse Transcriptase Polymerase Chain R

MESH TERMS: genetics

Chemical & Substance for Abstract: A two-stage binomial test approach of gene identification in oligonucleotide arrays. Information

Substance Name: Prolactin

Registry Number: 9002-62-4

Grant and Affiliation Information for A two-stage binomial test approach of gene identification in oligonucleotide arrays.

AFFILIATION: Biostatistics Division, Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, Florida 12902, USA. Dung-Tsa.Chen@moffitt.org

Country: United States

AGENCY: United States NIAID

GRANT: P30 AI 27767

ACRONYM: AI

MEDLINETA: J Biopharm Stat

REFSOURCE:

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