An analysis pipeline for the inference of protein-protein interaction networks

被引：3

作者：

Taylor, Ronald C. ^{[1
]}

Singhal, Mudita ^{[1
]}

Daly, Don S.

Gilmore, Jason ^{[2
]}

Cannon, William R.

Domico, Kelly ^{[3
]}

White, Amanda M.

Auberry, Deanna L.

Auberry, Kenneth J.

Hooker, Brian S.

Hurst, Greg ^{[4
]}

McDermott, Jason E.

McDonald, W. Hayes ^{[5
]}

Pelletier, Dale A. ^{[4
]}

Schmoyer, Denise ^{[4
]}

Wiley, H. Steven

机构：

[1] US DOE, Pacific NW Natl Lab, Computat Sci & Math Div, Computat Biol & Bioinformat Grp, Richland, WA 99352 USA

[2] Dartmouth Hitchcock Med Ctr, Lebanon, NH 03756 USA

[3] Battelle Seattle Res Ctr, Pacific NW Natl Lab, Seattle, WA 98109 USA

[4] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA

[5] Vanderbilt Univ, Sch Med, Mass Spectrometry Res Ctr, Nashville, TN 37232 USA

来源：

INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS | 2009年 / 3卷 / 04期

关键词：

network inference pipeline; protein-protein interactions; networks; MS; mass spectrometry; Bayesian; REGULATORY NETWORKS; DATABASE; ANNOTATION; BIOVERSE;

D O I：

10.1504/IJDMB.2009.029204

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We present a platform for the reconstruction of protein-protein interaction networks inferred from Mass Spectrometry (MS) bait-prey data. The Software Environment for Biological Network Inference (SEBINI), an environment for the deployment of network inference algorithms that use high-throughput data, forms the platform core. Among the many algorithms available in SEBINI is the Bayesian Estimator of Probabilities of Protein-Protein Associations (BEPro3) algorithm, which is used to infer interaction networks from such MS affinity isolation data. Also, the pipeline incorporates the Collective Analysis of Biological Interaction Networks (CABIN) software. We have thus created a structured workflow for protein-protein network inference and supplemental analysis.

引用

页码：409 / 430

页数：22

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