CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias
<p>Motivation: Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Published: |
Oxford University Press
2017
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| _version_ | 1797099114735861760 |
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| author | Luecken, M Page, M Crosby, A Mason, S Reinert, G Deane, C |
| author_facet | Luecken, M Page, M Crosby, A Mason, S Reinert, G Deane, C |
| author_sort | Luecken, M |
| collection | OXFORD |
| description | <p>Motivation: Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favour communities of well-studied proteins.</p><p> Results: We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker’s ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities, and identifies functional modules that may correspond to more novel biology.</p><p> Availability: The CommWalker algorithm is freely available at opig.stats.ox.ac.uk/resources or as a docker image on the Docker Hub at hub.docker.com/r/lueckenmd/commwalker</p> |
| first_indexed | 2024-03-07T05:19:03Z |
| format | Journal article |
| id | oxford-uuid:de3d6dce-cf23-4b4e-b32b-7fd163c5de11 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T05:19:03Z |
| publishDate | 2017 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:de3d6dce-cf23-4b4e-b32b-7fd163c5de112022-03-27T09:30:51ZCommWalker: Correctly evaluating modules in molecular networks in light of annotation biasJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:de3d6dce-cf23-4b4e-b32b-7fd163c5de11Symplectic Elements at OxfordOxford University Press2017Luecken, MPage, MCrosby, AMason, SReinert, GDeane, C<p>Motivation: Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favour communities of well-studied proteins.</p><p> Results: We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker’s ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities, and identifies functional modules that may correspond to more novel biology.</p><p> Availability: The CommWalker algorithm is freely available at opig.stats.ox.ac.uk/resources or as a docker image on the Docker Hub at hub.docker.com/r/lueckenmd/commwalker</p> |
| spellingShingle | Luecken, M Page, M Crosby, A Mason, S Reinert, G Deane, C CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias |
| title | CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias |
| title_full | CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias |
| title_fullStr | CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias |
| title_full_unstemmed | CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias |
| title_short | CommWalker: Correctly evaluating modules in molecular networks in light of annotation bias |
| title_sort | commwalker correctly evaluating modules in molecular networks in light of annotation bias |
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