F-MAP: A Bayesian approach to infer the gene regulatory network using external hints.
The Common topological features of related species gene regulatory networks suggest reconstruction of the network of one species by using the further information from gene expressions profile of related species. We present an algorithm to reconstruct the gene regulatory network named; F-MAP, which a...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5609748?pdf=render |
| _version_ | 1818990629739298816 |
|---|---|
| author | Maryam Shahdoust Hamid Pezeshk Hossein Mahjub Mehdi Sadeghi |
| author_facet | Maryam Shahdoust Hamid Pezeshk Hossein Mahjub Mehdi Sadeghi |
| author_sort | Maryam Shahdoust |
| collection | DOAJ |
| description | The Common topological features of related species gene regulatory networks suggest reconstruction of the network of one species by using the further information from gene expressions profile of related species. We present an algorithm to reconstruct the gene regulatory network named; F-MAP, which applies the knowledge about gene interactions from related species. Our algorithm sets a Bayesian framework to estimate the precision matrix of one species microarray gene expressions dataset to infer the Gaussian Graphical model of the network. The conjugate Wishart prior is used and the information from related species is applied to estimate the hyperparameters of the prior distribution by using the factor analysis. Applying the proposed algorithm on six related species of drosophila shows that the precision of reconstructed networks is improved considerably compared to the precision of networks constructed by other Bayesian approaches. |
| first_indexed | 2024-12-20T19:57:25Z |
| format | Article |
| id | doaj.art-772066063acc4a99b2898cfe885723f8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T19:57:25Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-772066063acc4a99b2898cfe885723f82022-12-21T19:28:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01129e018479510.1371/journal.pone.0184795F-MAP: A Bayesian approach to infer the gene regulatory network using external hints.Maryam ShahdoustHamid PezeshkHossein MahjubMehdi SadeghiThe Common topological features of related species gene regulatory networks suggest reconstruction of the network of one species by using the further information from gene expressions profile of related species. We present an algorithm to reconstruct the gene regulatory network named; F-MAP, which applies the knowledge about gene interactions from related species. Our algorithm sets a Bayesian framework to estimate the precision matrix of one species microarray gene expressions dataset to infer the Gaussian Graphical model of the network. The conjugate Wishart prior is used and the information from related species is applied to estimate the hyperparameters of the prior distribution by using the factor analysis. Applying the proposed algorithm on six related species of drosophila shows that the precision of reconstructed networks is improved considerably compared to the precision of networks constructed by other Bayesian approaches.http://europepmc.org/articles/PMC5609748?pdf=render |
| spellingShingle | Maryam Shahdoust Hamid Pezeshk Hossein Mahjub Mehdi Sadeghi F-MAP: A Bayesian approach to infer the gene regulatory network using external hints. PLoS ONE |
| title | F-MAP: A Bayesian approach to infer the gene regulatory network using external hints. |
| title_full | F-MAP: A Bayesian approach to infer the gene regulatory network using external hints. |
| title_fullStr | F-MAP: A Bayesian approach to infer the gene regulatory network using external hints. |
| title_full_unstemmed | F-MAP: A Bayesian approach to infer the gene regulatory network using external hints. |
| title_short | F-MAP: A Bayesian approach to infer the gene regulatory network using external hints. |
| title_sort | f map a bayesian approach to infer the gene regulatory network using external hints |
| url | http://europepmc.org/articles/PMC5609748?pdf=render |
| work_keys_str_mv | AT maryamshahdoust fmapabayesianapproachtoinferthegeneregulatorynetworkusingexternalhints AT hamidpezeshk fmapabayesianapproachtoinferthegeneregulatorynetworkusingexternalhints AT hosseinmahjub fmapabayesianapproachtoinferthegeneregulatorynetworkusingexternalhints AT mehdisadeghi fmapabayesianapproachtoinferthegeneregulatorynetworkusingexternalhints |