Redundancy Control in Pathway Databases (ReCiPa): An Application for Improving Gene-Set Enrichment Analysis in Omics Studies and “Big Data” Biology

Vivar, Juan C.; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

doi:10.1089/omi.2012.0083

Cited by 39 publications

(33 citation statements)

References 34 publications

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“…O mics is a systems science raising both promises and challenges from cell to society to bioeconomy (Akondi and Lakshmi, 2013;Bernabò et al, 2013;Birch and Tyfield, 2013;Bowler et al, 2013;Dove, 2013;Rajan, 2013;Vivar et al, 2013). A key challenge and opportunity is the rapid growth of published literature that makes biomedical text mining increasingly invaluable so as to unpack implicit knowledge hidden in unstructured text.…”

Section: Introductionmentioning

confidence: 99%

Network Analyses of Sperm–Egg Recognition and Binding: Ready to Rethink Fertility Mechanisms?

Bernabò

Ordinelli

Agostino

et al. 2014

OMICS: A Journal of Integrative Biology

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The rapid growth of published literature makes biomedical text mining increasingly invaluable for unpacking implicit knowledge hidden in unstructured text. We employed biomedical text mining and biological networks analyses to research the process of sperm egg recognition and binding (SERB). We selected from the literature the molecules expressed either on spermatozoa or on oocytes thought to be involved in SERB and, using an automated literature search software (Agilent Literature Search), we realized a network, SERBN, characterized by a hierarchical scale free and a small world topology. We used an integrated approach, either based on selection of hubs or by a cluster analysis, to discern the key molecules of SERB. We found that in most cases some of them are not directly situated on spermatozoa and oocyte, but are dispersed in oviductal fluid or embedded in exosomes present in the perivitelline space. To confirm and validate our results, we performed further analyses using STRING and Reactome FI software. Our findings underscore that the fertility is not a property of gametes in isolation, but rather depends on the functional integrity of the entire reproductive system. These observations collectively underscore the importance of integrative biology in exploring biological systems and in rethinking of fertility mechanisms in the light of this innovative approach.

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Section: Introductionmentioning

confidence: 99%

Network Analyses of Sperm–Egg Recognition and Binding: Ready to Rethink Fertility Mechanisms?

Bernabò

Ordinelli

Agostino

et al. 2014

OMICS: A Journal of Integrative Biology

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“…In support of that, despite the evidence about the relationship of CYP2D6 and drug response [6], the combined use of parallel alternate metabolic CYP pathways [23] that can compensate in the case of CYP2D6 PMs to individualize treatments with certain CYP2D6 sub- strates is, as yet, very limited, as is use of other genes such as those encoding drug receptors also involved in response [24]. Finally, individualized therapy to increase drug safety in different populations will also largely benefit from collecting and interrogating large genomics datasets in order to identify biological mechanisms associated with observed outcomes [25].…”

Section: Discussionmentioning

confidence: 99%

CYP2D6 Genetic Polymorphisms in Southern Mexican Mayan Lacandones and Mestizos from Chiapas

et al. 2014

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“…Our developed mapping strategy between different graph representations of analogous pathways enabled us to objectively compare pathway enrichment results that otherwise would have been conducted manually and subjectively. Furthermore, they allowed us to generate super pathways inspired by previous approaches that have shown the benefit of merging similar pathway representations (Stoney et al, 2018;Vivar et al, 2013;Doderer et al, 2012;Belinky et al, 2015). In this case, this was made possible by the fully harmonized gene sets and networks generated by our previous work, ComPath and PathMe.…”

Section: /21mentioning

confidence: 99%

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

Mubeen

Hoyt

Gemünd

et al. 2019

Preprint

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Background: 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. Results: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 database: 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 performance of machine learning models on different prediction tasks. Further, MPath significantly improved prediction performance and reduced the variance of prediction performances in some cases. At the same time, MPath yielded more consistent and biologically plausible results in the statistical enrichment analyses. Finally, we implemented a software package designed to make our comparative analysis with these and additional databases fully reproducible and to facilitate the update of our integrative pathway resource in the future. Conclusion:This benchmarking study demonstrates that pathway database choice can influence the results of statistical enrichment analysis and prediction modeling. Therefore, we recommend the use of multiple pathway databases or the use of integrative databases. 2/21

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Redundancy Control in Pathway Databases (ReCiPa): An Application for Improving Gene-Set Enrichment Analysis in Omics Studies and “Big Data” Biology

Cited by 39 publications

References 34 publications

Network Analyses of Sperm–Egg Recognition and Binding: Ready to Rethink Fertility Mechanisms?

Network Analyses of Sperm–Egg Recognition and Binding: Ready to Rethink Fertility Mechanisms?

CYP2D6 Genetic Polymorphisms in Southern Mexican Mayan Lacandones and Mestizos from Chiapas

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

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