A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases.
Increasing evidence has indicated that long non-coding RNAs (lncRNAs) are implicated in and associated with many complex human diseases. Despite of the accumulation of lncRNA-disease associations, only a few studies had studied the roles of these associations in pathogenesis. In this paper, we inves...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3909255?pdf=render |
| _version_ | 1818932454036078592 |
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| author | Xiaofei Yang Lin Gao Xingli Guo Xinghua Shi Hao Wu Fei Song Bingbo Wang |
| author_facet | Xiaofei Yang Lin Gao Xingli Guo Xinghua Shi Hao Wu Fei Song Bingbo Wang |
| author_sort | Xiaofei Yang |
| collection | DOAJ |
| description | Increasing evidence has indicated that long non-coding RNAs (lncRNAs) are implicated in and associated with many complex human diseases. Despite of the accumulation of lncRNA-disease associations, only a few studies had studied the roles of these associations in pathogenesis. In this paper, we investigated lncRNA-disease associations from a network view to understand the contribution of these lncRNAs to complex diseases. Specifically, we studied both the properties of the diseases in which the lncRNAs were implicated, and that of the lncRNAs associated with complex diseases. Regarding the fact that protein coding genes and lncRNAs are involved in human diseases, we constructed a coding-non-coding gene-disease bipartite network based on known associations between diseases and disease-causing genes. We then applied a propagation algorithm to uncover the hidden lncRNA-disease associations in this network. The algorithm was evaluated by leave-one-out cross validation on 103 diseases in which at least two genes were known to be involved, and achieved an AUC of 0.7881. Our algorithm successfully predicted 768 potential lncRNA-disease associations between 66 lncRNAs and 193 diseases. Furthermore, our results for Alzheimer's disease, pancreatic cancer, and gastric cancer were verified by other independent studies. |
| first_indexed | 2024-12-20T04:32:44Z |
| format | Article |
| id | doaj.art-c2203edb9ff24cb495aed4e0c23c062c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T04:32:44Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c2203edb9ff24cb495aed4e0c23c062c2022-12-21T19:53:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0191e8779710.1371/journal.pone.0087797A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases.Xiaofei YangLin GaoXingli GuoXinghua ShiHao WuFei SongBingbo WangIncreasing evidence has indicated that long non-coding RNAs (lncRNAs) are implicated in and associated with many complex human diseases. Despite of the accumulation of lncRNA-disease associations, only a few studies had studied the roles of these associations in pathogenesis. In this paper, we investigated lncRNA-disease associations from a network view to understand the contribution of these lncRNAs to complex diseases. Specifically, we studied both the properties of the diseases in which the lncRNAs were implicated, and that of the lncRNAs associated with complex diseases. Regarding the fact that protein coding genes and lncRNAs are involved in human diseases, we constructed a coding-non-coding gene-disease bipartite network based on known associations between diseases and disease-causing genes. We then applied a propagation algorithm to uncover the hidden lncRNA-disease associations in this network. The algorithm was evaluated by leave-one-out cross validation on 103 diseases in which at least two genes were known to be involved, and achieved an AUC of 0.7881. Our algorithm successfully predicted 768 potential lncRNA-disease associations between 66 lncRNAs and 193 diseases. Furthermore, our results for Alzheimer's disease, pancreatic cancer, and gastric cancer were verified by other independent studies.http://europepmc.org/articles/PMC3909255?pdf=render |
| spellingShingle | Xiaofei Yang Lin Gao Xingli Guo Xinghua Shi Hao Wu Fei Song Bingbo Wang A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. PLoS ONE |
| title | A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. |
| title_full | A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. |
| title_fullStr | A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. |
| title_full_unstemmed | A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. |
| title_short | A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. |
| title_sort | network based method for analysis of lncrna disease associations and prediction of lncrnas implicated in diseases |
| url | http://europepmc.org/articles/PMC3909255?pdf=render |
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