Name
Title | ||
|---|---|---|
SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction |
Abstract | ||
|---|---|---|
The Software Environment for BIological Network Inference (SEBINI) has been created to provide an interactive environment for the deployment and testing of network inference algorithms that use high-throughput expression data. Networks inferred from the SEBINI software platform can be further analyzed using the Collective Analysis of Biological Interaction Networks (CABIN), software that allows integration and analysis of proteinprotein interaction and gene-to-gene regulatory evidence obtained from multiple sources. In this paper, we present a case study on the SEBINI and CABIN tools for protein-protein interaction network reconstruction. Incorporating the Bayesian Estimator of Protein-Protein Association Probabilities (BEPro) algorithm into the SEBINI toolkit, we have created a pipeline for structural inference and supplemental analysis of proteinprotein interaction networks from sets of mass spectrometry bait-prey experiment data. Demo site for SEBINI: https://www.emsl.pnl.gov /SEBINI/ Contact: ronald.taylor@pnl.gov The BEPro algorithm is available at http://www.pnl.gov/statistics/BEPro3/index.htm. Contact: ds.daly@pnl.gov. CABIN can be downloaded from www.sysbio.org/dataresources/ cabin.stm. Contact: mudita.singhal@pnl.gov. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1109/ICMLA.2007.92 | ICMLA |
Keywords | Field | DocType |
interaction network,algorithms,proteins,mass spectrometry,biological network inference,interactions,data analysis,high throughput,genes,genetics,biological network,protein protein interaction | Protein protein interaction network,Data mining,Software deployment,Protein Interaction Networks,Inference,Computer science,Interaction network,Software,Bayesian estimator,Artificial intelligence,Biological network inference,Machine learning | Conference |
ISBN | Citations | PageRank |
0-7695-3069-9 | 1 | 0.42 |
References | Authors | |
11 | 14 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Ronald C. Taylor | 1 | 238 | 19.01 |
| Mudita Singhal | 2 | 475 | 40.59 |
| Don Simone Daly | 3 | 19 | 3.98 |
| Kelly Domico | 4 | 17 | 2.20 |
| Amanda M. White | 5 | 29 | 5.94 |
| Deanna L. Auberry | 6 | 6 | 1.25 |
| Kenneth J. Auberry | 7 | 7 | 1.50 |
| Brian Hooker | 8 | 4 | 1.20 |
| Gregory B. Hurst | 9 | 7 | 2.32 |
| Jason E. McDermott | 10 | 1 | 0.75 |
| W. Hayes McDonald | 11 | 39 | 6.90 |
| Dale Pelletier | 12 | 6 | 1.26 |
| Denise Schmoyer | 13 | 96 | 12.81 |
| William R. Cannon | 14 | 69 | 10.68 |