ComHub: Community predictions of hubs in gene regulatory networks
Abstract Background Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expre...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-02-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-03987-y |
| _version_ | 1818417511353286656 |
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| author | Julia Åkesson Zelmina Lubovac-Pilav Rasmus Magnusson Mika Gustafsson |
| author_facet | Julia Åkesson Zelmina Lubovac-Pilav Rasmus Magnusson Mika Gustafsson |
| author_sort | Julia Åkesson |
| collection | DOAJ |
| description | Abstract Background Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expression data, few methods focus on inferring these hubs. Results We have developed ComHub, a tool to predict hubs in GRNs. ComHub makes a community prediction of hubs by averaging over predictions by a compendium of network inference methods. Benchmarking ComHub against the DREAM5 challenge data and two independent gene expression datasets showed a robust performance of ComHub over all datasets. Conclusions In contrast to other evaluated methods, ComHub consistently scored among the top performing methods on data from different sources. Lastly, we implemented ComHub to work with both predefined networks and to perform stand-alone network inference, which will make the method generally applicable. |
| first_indexed | 2024-12-14T12:07:57Z |
| format | Article |
| id | doaj.art-51847f738ca64ffbb7864a3ac19c54ea |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-14T12:07:57Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-51847f738ca64ffbb7864a3ac19c54ea2022-12-21T23:01:50ZengBMCBMC Bioinformatics1471-21052021-02-0122111210.1186/s12859-021-03987-yComHub: Community predictions of hubs in gene regulatory networksJulia Åkesson0Zelmina Lubovac-Pilav1Rasmus Magnusson2Mika Gustafsson3Department of Physics, Chemistry and Biology, Linköping UniversitySystems Biology Research Centre, School of bioscience, University of SkövdeDepartment of Physics, Chemistry and Biology, Linköping UniversityDepartment of Physics, Chemistry and Biology, Linköping UniversityAbstract Background Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expression data, few methods focus on inferring these hubs. Results We have developed ComHub, a tool to predict hubs in GRNs. ComHub makes a community prediction of hubs by averaging over predictions by a compendium of network inference methods. Benchmarking ComHub against the DREAM5 challenge data and two independent gene expression datasets showed a robust performance of ComHub over all datasets. Conclusions In contrast to other evaluated methods, ComHub consistently scored among the top performing methods on data from different sources. Lastly, we implemented ComHub to work with both predefined networks and to perform stand-alone network inference, which will make the method generally applicable.https://doi.org/10.1186/s12859-021-03987-yGene regulatory networksHubsMaster regulatorsNetwork inference |
| spellingShingle | Julia Åkesson Zelmina Lubovac-Pilav Rasmus Magnusson Mika Gustafsson ComHub: Community predictions of hubs in gene regulatory networks BMC Bioinformatics Gene regulatory networks Hubs Master regulators Network inference |
| title | ComHub: Community predictions of hubs in gene regulatory networks |
| title_full | ComHub: Community predictions of hubs in gene regulatory networks |
| title_fullStr | ComHub: Community predictions of hubs in gene regulatory networks |
| title_full_unstemmed | ComHub: Community predictions of hubs in gene regulatory networks |
| title_short | ComHub: Community predictions of hubs in gene regulatory networks |
| title_sort | comhub community predictions of hubs in gene regulatory networks |
| topic | Gene regulatory networks Hubs Master regulators Network inference |
| url | https://doi.org/10.1186/s12859-021-03987-y |
| work_keys_str_mv | AT juliaakesson comhubcommunitypredictionsofhubsingeneregulatorynetworks AT zelminalubovacpilav comhubcommunitypredictionsofhubsingeneregulatorynetworks AT rasmusmagnusson comhubcommunitypredictionsofhubsingeneregulatorynetworks AT mikagustafsson comhubcommunitypredictionsofhubsingeneregulatorynetworks |