Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond
Abstract Background Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks, provide a natural way to integrate diverse and multi-scale data sourc...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-024-05683-z |
| _version_ | 1797273050257817600 |
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| author | Anthony Baptista Galadriel Brière Anaïs Baudot |
| author_facet | Anthony Baptista Galadriel Brière Anaïs Baudot |
| author_sort | Anthony Baptista |
| collection | DOAJ |
| description | Abstract Background Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks, provide a natural way to integrate diverse and multi-scale data sources into a common framework. Recently, we developed MultiXrank, a Random Walk with Restart algorithm able to explore such multilayer networks. MultiXrank outputs scores reflecting the proximity between an initial set of seed node(s) and all the other nodes in the multilayer network. We illustrate here the versatility of bioinformatics tasks that can be performed using MultiXrank. Results We first show that MultiXrank can be used to prioritise genes and drugs of interest by exploring multilayer networks containing interactions between genes, drugs, and diseases. In a second study, we illustrate how MultiXrank scores can also be used in a supervised strategy to train a binary classifier to predict gene-disease associations. The classifier performance are validated using outdated and novel gene-disease association for training and evaluation, respectively. Finally, we show that MultiXrank scores can be used to compute diffusion profiles and use them as disease signatures. We computed the diffusion profiles of more than 100 immune diseases using a multilayer network that includes cell-type specific genomic information. The clustering of the immune disease diffusion profiles reveals shared shared phenotypic characteristics. Conclusion Overall, we illustrate here diverse applications of MultiXrank to showcase its versatility. We expect that this can lead to further and broader bioinformatics applications. |
| first_indexed | 2024-03-07T14:37:58Z |
| format | Article |
| id | doaj.art-9f1e34c21ed543a08beaa9d321659347 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-07T14:37:58Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9f1e34c21ed543a08beaa9d3216593472024-03-05T20:31:53ZengBMCBMC Bioinformatics1471-21052024-02-0125111910.1186/s12859-024-05683-zRandom walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyondAnthony Baptista0Galadriel Brière1Anaïs Baudot2School of Mathematical Sciences, Queen Mary University of LondonCNRS, I2M, Aix-Marseille UnivINSERM, MMG, Turing Center for Living Systems, Aix-Marseille UnivAbstract Background Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks, provide a natural way to integrate diverse and multi-scale data sources into a common framework. Recently, we developed MultiXrank, a Random Walk with Restart algorithm able to explore such multilayer networks. MultiXrank outputs scores reflecting the proximity between an initial set of seed node(s) and all the other nodes in the multilayer network. We illustrate here the versatility of bioinformatics tasks that can be performed using MultiXrank. Results We first show that MultiXrank can be used to prioritise genes and drugs of interest by exploring multilayer networks containing interactions between genes, drugs, and diseases. In a second study, we illustrate how MultiXrank scores can also be used in a supervised strategy to train a binary classifier to predict gene-disease associations. The classifier performance are validated using outdated and novel gene-disease association for training and evaluation, respectively. Finally, we show that MultiXrank scores can be used to compute diffusion profiles and use them as disease signatures. We computed the diffusion profiles of more than 100 immune diseases using a multilayer network that includes cell-type specific genomic information. The clustering of the immune disease diffusion profiles reveals shared shared phenotypic characteristics. Conclusion Overall, we illustrate here diverse applications of MultiXrank to showcase its versatility. We expect that this can lead to further and broader bioinformatics applications.https://doi.org/10.1186/s12859-024-05683-zMultilayer networkRandom walk with restartMulti-omics dataBiological network |
| spellingShingle | Anthony Baptista Galadriel Brière Anaïs Baudot Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond BMC Bioinformatics Multilayer network Random walk with restart Multi-omics data Biological network |
| title | Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond |
| title_full | Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond |
| title_fullStr | Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond |
| title_full_unstemmed | Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond |
| title_short | Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond |
| title_sort | random walk with restart on multilayer networks from node prioritisation to supervised link prediction and beyond |
| topic | Multilayer network Random walk with restart Multi-omics data Biological network |
| url | https://doi.org/10.1186/s12859-024-05683-z |
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