Name
Abstract | ||
|---|---|---|
Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the existing methods to small signaling networks of size 10-15 genes. In this paper, we propose integrating RNAi data with a reference physical interaction network. We formulate the problem of signaling network reconstruction as finding the minimum number of edit operations on a given reference network. The edit operations transform the reference network to a network that satisfies the RNAi observations. We show that using a reference network does not simplify the computational complexity of the problem. Therefore, we propose two methods which provide near optimal results and can scale well for reconstructing networks up to hundreds of components. We validate the proposed methods on synthetic and real data sets. Comparison with the state of the art on real signaling networks shows that the proposed methodology can scale better and generates biologically significant results. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1109/TCBB.2012.128 | IEEE/ACM Trans. Comput. Biology Bioinform. |
Keywords | Field | DocType |
network reconstruction,rnai observation,rnai data,reference physical interaction network,underdetermined problem,large-scale signaling network reconstruction,rna interference,proposed methodology,reference network,molecular biophysics,computational complexity,genomics,computational biology,rna,proteins,topology,bioinformatics,rnai,network topology,genetics | Data set,Physical interaction,Underdetermined system,Exponential search,Computer science,Signaling network,Network topology,Bioinformatics,Synthetic data sets,Computational complexity theory | Journal |
Volume | Issue | ISSN |
9 | 6 | 1557-9964 |
Citations | PageRank | References |
2 | 0.44 | 2 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Seyedsasan Hashemikhabir | 1 | 3 | 1.83 |
| Eyup Serdar Ayaz | 2 | 2 | 0.44 |
| Yusuf Kavurucu | 3 | 77 | 7.82 |
| Tolga Can | 4 | 268 | 16.39 |
| Tamer Kahveci | 5 | 537 | 61.50 |