Name
Title | ||
|---|---|---|
Improving the accuracy of signal transduction pathway construction using level-2 neighbours |
Abstract | ||
|---|---|---|
In this paper, we consider the problem of reconstructing a pathway for a given set of proteins based on available genomics and proteomics information such as gene expression data. In all previous approaches, the scoring function for a candidate pathway usually only depends on adjacent proteins in the pathway. We propose to also consider proteins that are of distance two in the pathway (we call them Level-2 neighbours). We derive a scoring function based on both adjacent proteins and Level-2 neighbours in the pathway and show that our scoring function can increase the accuracy of the predicted pathways through a set of experiments. The problem of computing the pathway with optimal score, in general, is NP-hard. We thus extend a randomised algorithm to make it work on our scoring function to compute the optimal pathway with high probability. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1504/IJBRA.2010.038736 | International journal of bioinformatics research and applications |
Keywords | DocType | Volume |
level-2 neighbour,optimal score,high probability,gene expression data,signal transduction pathway construction,adjacent protein,scoring function,available genomics,candidate pathway,previous approach,optimal pathway | Journal | 6 |
Issue | ISSN | Citations |
6 | 1744-5485 | 0 |
PageRank | References | Authors |
0.34 | 3 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Thomas K. F. Wong | 1 | 89 | 9.80 |
| Tak-Wah Lam | 2 | 1860 | 164.96 |
| S. M. Yiu | 3 | 0 | 0.34 |
| Simon Wong | 4 | 138 | 11.68 |