Abstract:
:Pathway-centric approaches are widely used to interpret and contextualize -omics data. However, databases contain different representations of the same biological pathway, which may lead to different results of statistical enrichment analysis and predictive models in the context of precision medicine. We have performed an in-depth benchmarking of the impact of pathway database choice on statistical enrichment analysis and predictive modeling. We analyzed five cancer datasets using three major pathway databases and developed an approach to merge several databases into a single integrative one: MPath. Our results show that equivalent pathways from different databases yield disparate results in statistical enrichment analysis. Moreover, we observed a significant dataset-dependent impact on the performance of machine learning models on different prediction tasks. In some cases, MPath significantly improved prediction performance and also reduced the variance of prediction performances. Furthermore, MPath yielded more consistent and biologically plausible results in statistical enrichment analyses. In summary, this benchmarking study demonstrates that pathway database choice can influence the results of statistical enrichment analysis and predictive modeling. Therefore, we recommend the use of multiple pathway databases or integrative ones.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Mubeen S,Hoyt CT,Gemünd A,Hofmann-Apitius M,Fröhlich H,Domingo-Fernández Ddoi
10.3389/fgene.2019.01203subject
Has Abstractpub_date
2019-11-22 00:00:00pages
1203issn
1664-8021journal_volume
10pub_type
杂志文章abstract::Background: Milroy disease (MD) is rare and autosomal dominant resulting from mutations of the vascular endothelial growth factor receptor-3 (VEGFR-3 or FLT4), which leads to dysgenesis of the lymphatic system. Methods: Here we report a Chinese MD family with 2 affected members of two generations. We identified the mu...
journal_title:Frontiers in genetics
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更新日期:2019-03-19 00:00:00
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pub_type: 杂志文章
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pub_type: 杂志文章
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abstract::Obesity has become a major public health issue which is caused by a combination of genetic and environmental factors. Genome-wide DNA methylation studies have identified that DNA methylation at Cytosine-phosphate-Guanine (CpG) sites are associated with obesity. However, subsequent functional validation of the results ...
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pub_type: 杂志文章,评审
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01165
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pub_type: 杂志文章
doi:10.3389/fgene.2015.00193
更新日期:2015-05-27 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00159
更新日期:2014-06-03 00:00:00
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doi:10.3389/fgene.2020.00154
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doi:10.3389/fgene.2020.608517
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pub_type: 杂志文章,评审
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pub_type: 杂志文章
doi:10.3389/fgene.2020.00769
更新日期:2020-08-04 00:00:00
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