Analyzing marginal cases in differential shotgun proteomics

被引：17

作者：

Carvalho, Paulo C. ^{[1
,2
]}

Fischer, Juliana S. G. ^{[1
,3
]}

Perales, Jonas ^{[2
]}

Yates, John R. ^{[4
]}

Barbosa, Valmir C. ^{[5
]}

Bareinboim, Elias ^{[6
]}

机构：

[1] Inst Oswaldo Cruz, Ctr Technol Dev Hlth, BR-20001 Rio De Janeiro, Brazil

[2] Inst Oswaldo Cruz, Dept Physiol & Pharmacodynam, Lab Toxinol, BR-20001 Rio De Janeiro, Brazil

[3] Inst Oswaldo Cruz, Dept Biochem & Mol Biol, Lab Funct Genom & Bioinformat, BR-20001 Rio De Janeiro, Brazil

[4] Scripps Res Inst, Dept Physiol Chem, La Jolla, CA 92037 USA

[5] Univ Fed Rio de Janeiro, Syst Engn & Comp Sci Program, Rio De Janeiro, Brazil

[6] Univ Calif Los Angeles, Dept Comp Sci, Los Angeles, CA 90024 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 02期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/btq632

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We present an approach to statistically pinpoint differentially expressed proteins that have quantitation values near the quantitation threshold and are not identified in all replicates (marginal cases). Our method uses a Bayesian strategy to combine parametric statistics with an empirical distribution built from the reproducibility quality of the technical replicates.

引用

页码：275 / 276

页数：2

共 5 条

[1]

Carvalho Paulo C, 2010, Curr Protoc Bioinformatics, VChapter 13, DOI 10.1002/0471250953.bi1313s30

[2] PatternLab for proteomics: a tool for differential shotgun proteomics [J].

Carvalho, Paulo C. ;

Fischer, Juliana Sg ;

Chen, Emily I. ;

Yates, John R., III ;

Barbosa, Valmir C. .

BMC BIOINFORMATICS, 2008, 9 (1)

[3] Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol [J].

da Gama Fischer, Juliana de Saldanha ;

Liao, Lujian ;

Carvalho, Paulo C. ;

Barbosa, Valmir C. ;

Domont, Gilberto B. ;

da Costa Carvalho, Maria da Gloria ;

Yates, John R., III .

JOURNAL OF PROTEOMICS, 2010, 73 (05) :1018-1027

[4] A model for random sampling and estimation of relative protein abundance in shotgun proteomics [J].

Liu, HB ;

Sadygov, RG ;

Yates, JR .

ANALYTICAL CHEMISTRY, 2004, 76 (14) :4193-4201

[5] Large-scale analysis of the yeast proteome by multidimensional protein identification technology [J].

Washburn, MP ;

Wolters, D ;

Yates, JR .

NATURE BIOTECHNOLOGY, 2001, 19 (03) :242-247

← 1 →