An analysis pipeline for the inference of protein-protein interaction networks.
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.
Taylor
Ronald C
RC
Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory (US Department of Energy), Richland, WA 99352, USA. ronald.taylor@pnl.gov
Singhal
Mudita
M
Daly
Don S
DS
Gilmore
Jason
J
Cannon
William R
WR
Domico
Kelly
K
White
Amanda M
AM
Auberry
Deanna L
DL
Auberry
Kenneth J
KJ
Hooker
Brian S
BS
Hurst
Greg
G
McDermott
Jason E
JE
McDonald
W Hayes
WH
Pelletier
Dale A
DA
Schmoyer
Denise
D
Wiley
H Steven
HS
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
D011506:Proteins