ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations]
Contextual functional interpretation of -omics data derived from clinical samples is a classical and difficult problem in computational systems biology. The measurement of thousands of data points on single samples has become routine but relating ‘big data’ datasets to the complexities of human path...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wellcome
2018-06-01
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| Series: | Wellcome Open Research |
| Online Access: | https://wellcomeopenresearch.org/articles/3-27/v2 |
| _version_ | 1818276825307021312 |
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| author | Armin Deffur Robert J. Wilkinson Bongani M. Mayosi Nicola M. Mulder |
| author_facet | Armin Deffur Robert J. Wilkinson Bongani M. Mayosi Nicola M. Mulder |
| author_sort | Armin Deffur |
| collection | DOAJ |
| description | Contextual functional interpretation of -omics data derived from clinical samples is a classical and difficult problem in computational systems biology. The measurement of thousands of data points on single samples has become routine but relating ‘big data’ datasets to the complexities of human pathobiology is an area of ongoing research. Complicating this is the fact that many publicly available datasets use bulk transcriptomics data from complex tissues like blood. The most prevalent analytic approaches derive molecular ‘signatures’ of disease states or apply modular analysis frameworks to the data. Here we describe ANIMA (association network integration for multiscale analysis), a network-based data integration method using clinical phenotype and microarray data as inputs. ANIMA is implemented in R and Neo4j and runs in Docker containers. In short, the build algorithm iterates over one or more transcriptomics datasets to generate a large, multipartite association network by executing multiple independent analytic steps (differential expression, deconvolution, modular analysis based on co-expression, pathway analysis) and integrating the results. Once the network is built, it can be queried directly using Cypher (a graph query language), or by custom functions that communicate with the graph database via language-specific APIs. We developed a web application using Shiny, which provides fully interactive, multiscale views of the data. Using our approach, we show that we can reconstruct multiple features of disease states at various scales of organization, from transcript abundance patterns of individual genes through co-expression patterns of groups of genes to patterns of cellular behaviour in whole blood samples, both in single experiments as well in meta-analyses of multiple datasets. |
| first_indexed | 2024-12-12T22:51:48Z |
| format | Article |
| id | doaj.art-b251e4530b8041369ef688b76c910202 |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-12-12T22:51:48Z |
| publishDate | 2018-06-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj.art-b251e4530b8041369ef688b76c9102022022-12-22T00:09:03ZengWellcomeWellcome Open Research2398-502X2018-06-01310.12688/wellcomeopenres.14073.215932ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations]Armin Deffur0Robert J. Wilkinson1Bongani M. Mayosi2Nicola M. Mulder3Department of Medicine, University of Cape Town, Cape Town, 7925, South AfricaDepartment of Medicine, University of Cape Town, Cape Town, 7925, South AfricaDepartment of Medicine, University of Cape Town, Cape Town, 7925, South AfricaComputational Biology Division, Department Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, 7925, South AfricaContextual functional interpretation of -omics data derived from clinical samples is a classical and difficult problem in computational systems biology. The measurement of thousands of data points on single samples has become routine but relating ‘big data’ datasets to the complexities of human pathobiology is an area of ongoing research. Complicating this is the fact that many publicly available datasets use bulk transcriptomics data from complex tissues like blood. The most prevalent analytic approaches derive molecular ‘signatures’ of disease states or apply modular analysis frameworks to the data. Here we describe ANIMA (association network integration for multiscale analysis), a network-based data integration method using clinical phenotype and microarray data as inputs. ANIMA is implemented in R and Neo4j and runs in Docker containers. In short, the build algorithm iterates over one or more transcriptomics datasets to generate a large, multipartite association network by executing multiple independent analytic steps (differential expression, deconvolution, modular analysis based on co-expression, pathway analysis) and integrating the results. Once the network is built, it can be queried directly using Cypher (a graph query language), or by custom functions that communicate with the graph database via language-specific APIs. We developed a web application using Shiny, which provides fully interactive, multiscale views of the data. Using our approach, we show that we can reconstruct multiple features of disease states at various scales of organization, from transcript abundance patterns of individual genes through co-expression patterns of groups of genes to patterns of cellular behaviour in whole blood samples, both in single experiments as well in meta-analyses of multiple datasets.https://wellcomeopenresearch.org/articles/3-27/v2 |
| spellingShingle | Armin Deffur Robert J. Wilkinson Bongani M. Mayosi Nicola M. Mulder ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations] Wellcome Open Research |
| title | ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations] |
| title_full | ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations] |
| title_fullStr | ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations] |
| title_full_unstemmed | ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations] |
| title_short | ANIMA: Association network integration for multiscale analysis [version 2; referees: 1 approved, 2 approved with reservations] |
| title_sort | anima association network integration for multiscale analysis version 2 referees 1 approved 2 approved with reservations |
| url | https://wellcomeopenresearch.org/articles/3-27/v2 |
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