PyBootNet: a python package for bootstrapping and network construction
Background Network analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data (e.g., genes and metabolites). Two aspects of networks that are difficult to assess are the...
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PeerJ Inc.
2025-02-01
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| Online Access: | https://peerj.com/articles/18915.pdf |
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| author | Shayan R. Akhavan Scott T. Kelley |
| author_facet | Shayan R. Akhavan Scott T. Kelley |
| author_sort | Shayan R. Akhavan |
| collection | DOAJ |
| description | Background Network analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data (e.g., genes and metabolites). Two aspects of networks that are difficult to assess are the statistical robustness of the network and whether networks from two different biological systems or experimental conditions differ. Methods PyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be accessible and efficient with minimal dependencies and straightforward input requirements. To demonstrate its functionality, we applied PyBootNet to compare correlation networks derived from study using a mouse model to investigate the impacts of Polycystic Ovary Syndrome (PCOS) on the gut microbiome. PyBootNet includes functions for data preprocessing, bootstrapping, correlation matrix calculation, network statistics computation, and network visualization. Results We show that PyBootNet generates robust bootstrapped network metrics and identifies significant differences in one or more network metrics between pairs of networks. Our analysis of the previously published PCOS gut microbiome data also showed that our network analysis uncovered patterns and treatment effects missed in the original study. PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbes, genes, metabolites and other biological data appropriate for network correlation comparison and analysis. |
| format | Article |
| id | doaj-art-8d457f66327f4b41b586584d752b3d85 |
| institution | Kabale University |
| issn | 2167-8359 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj-art-8d457f66327f4b41b586584d752b3d852025-02-07T15:05:10ZengPeerJ Inc.PeerJ2167-83592025-02-0113e1891510.7717/peerj.18915PyBootNet: a python package for bootstrapping and network constructionShayan R. Akhavan0Scott T. Kelley1Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of AmericaBioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of AmericaBackground Network analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data (e.g., genes and metabolites). Two aspects of networks that are difficult to assess are the statistical robustness of the network and whether networks from two different biological systems or experimental conditions differ. Methods PyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be accessible and efficient with minimal dependencies and straightforward input requirements. To demonstrate its functionality, we applied PyBootNet to compare correlation networks derived from study using a mouse model to investigate the impacts of Polycystic Ovary Syndrome (PCOS) on the gut microbiome. PyBootNet includes functions for data preprocessing, bootstrapping, correlation matrix calculation, network statistics computation, and network visualization. Results We show that PyBootNet generates robust bootstrapped network metrics and identifies significant differences in one or more network metrics between pairs of networks. Our analysis of the previously published PCOS gut microbiome data also showed that our network analysis uncovered patterns and treatment effects missed in the original study. PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbes, genes, metabolites and other biological data appropriate for network correlation comparison and analysis.https://peerj.com/articles/18915.pdfMicrobial communitiesComputational biologyBuilt environmentGut microbiomeNetwork metricsSoftware package |
| spellingShingle | Shayan R. Akhavan Scott T. Kelley PyBootNet: a python package for bootstrapping and network construction PeerJ Microbial communities Computational biology Built environment Gut microbiome Network metrics Software package |
| title | PyBootNet: a python package for bootstrapping and network construction |
| title_full | PyBootNet: a python package for bootstrapping and network construction |
| title_fullStr | PyBootNet: a python package for bootstrapping and network construction |
| title_full_unstemmed | PyBootNet: a python package for bootstrapping and network construction |
| title_short | PyBootNet: a python package for bootstrapping and network construction |
| title_sort | pybootnet a python package for bootstrapping and network construction |
| topic | Microbial communities Computational biology Built environment Gut microbiome Network metrics Software package |
| url | https://peerj.com/articles/18915.pdf |
| work_keys_str_mv | AT shayanrakhavan pybootnetapythonpackageforbootstrappingandnetworkconstruction AT scotttkelley pybootnetapythonpackageforbootstrappingandnetworkconstruction |