Analyzing marginal cases in differential shotgun proteomics

被引：16

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
Carvalho, Paulo C.
Fischer, Juliana Sg
Chen, Emily I.
Yates, John R., III
Barbosa, Valmir C.
[J]. BMC BIOINFORMATICS, 2008, 9 (1)
[3] Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol
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
[J]. JOURNAL OF PROTEOMICS, 2010, 73 (05) : 1018 - 1027
[4] A model for random sampling and estimation of relative protein abundance in shotgun proteomics
Liu, HB
Sadygov, RG
Yates, JR
[J]. ANALYTICAL CHEMISTRY, 2004, 76 (14) : 4193 - 4201
[5] Large-scale analysis of the yeast proteome by multidimensional protein identification technology
Washburn, MP
Wolters, D
Yates, JR
[J]. NATURE BIOTECHNOLOGY, 2001, 19 (03) : 242 - 247

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