Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms
With the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topolo...
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| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2012-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1100/2012/315797 |
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| _version_ | 1832552108595871744 |
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| author | Cheng-Yu Yeh Hsiang-Yuan Yeh Carlos Roberto Arias Von-Wun Soo |
| author_facet | Cheng-Yu Yeh Hsiang-Yuan Yeh Carlos Roberto Arias Von-Wun Soo |
| author_sort | Cheng-Yu Yeh |
| collection | DOAJ |
| description | With the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topology and applied heuristic search to speed up color-coding method. In the experiments, we tested our methods by applying to two datasets: yeast and human prostate cancer networks and gene expression data set. The comparisons of our method with other existing methods on known yeast MAPK pathways in terms of precision and recall show that we can find maximum number of the proteins and perform comparably well. On the other hand, our method is more efficient than previous ones and detects the paths of length 10 within 40 seconds using CPU Intel 1.73GHz and 1GB main memory running under windows operating system. |
| format | Article |
| id | doaj-art-0b5f47c216fb4de3a9dfb77379f78b57 |
| institution | Kabale University |
| issn | 1537-744X |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-0b5f47c216fb4de3a9dfb77379f78b572025-02-03T05:59:31ZengWileyThe Scientific World Journal1537-744X2012-01-01201210.1100/2012/315797315797Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search AlgorithmsCheng-Yu Yeh0Hsiang-Yuan Yeh1Carlos Roberto Arias2Von-Wun Soo3Department of Computer Science, National Tsing Hua University, Hsinchu 300, TaiwanDepartment of Computer Science, National Tsing Hua University, Hsinchu 300, TaiwanDepartment of Computer Science, National Tsing Hua University, Hsinchu 300, TaiwanDepartment of Computer Science, National Tsing Hua University, Hsinchu 300, TaiwanWith the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topology and applied heuristic search to speed up color-coding method. In the experiments, we tested our methods by applying to two datasets: yeast and human prostate cancer networks and gene expression data set. The comparisons of our method with other existing methods on known yeast MAPK pathways in terms of precision and recall show that we can find maximum number of the proteins and perform comparably well. On the other hand, our method is more efficient than previous ones and detects the paths of length 10 within 40 seconds using CPU Intel 1.73GHz and 1GB main memory running under windows operating system.http://dx.doi.org/10.1100/2012/315797 |
| spellingShingle | Cheng-Yu Yeh Hsiang-Yuan Yeh Carlos Roberto Arias Von-Wun Soo Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms The Scientific World Journal |
| title | Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms |
| title_full | Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms |
| title_fullStr | Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms |
| title_full_unstemmed | Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms |
| title_short | Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A* Search Algorithms |
| title_sort | pathway detection from protein interaction networks and gene expression data using color coding methods and a search algorithms |
| url | http://dx.doi.org/10.1100/2012/315797 |
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