Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective
Causal discovery is a highly promising tool with a broad perspective in the field of biology. In this study, a causal structure robustness assessment algorithm is proposed and employed on the causal structures obtained, based on transcriptomic, proteomic, and the combined datasets, emerging from a q...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/14/1/8 |
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| author | Maria Ganopoulou Aliki Xanthopoulou Michail Michailidis Lefteris Angelis Ioannis Ganopoulos Theodoros Moysiadis |
| author_facet | Maria Ganopoulou Aliki Xanthopoulou Michail Michailidis Lefteris Angelis Ioannis Ganopoulos Theodoros Moysiadis |
| author_sort | Maria Ganopoulou |
| collection | DOAJ |
| description | Causal discovery is a highly promising tool with a broad perspective in the field of biology. In this study, a causal structure robustness assessment algorithm is proposed and employed on the causal structures obtained, based on transcriptomic, proteomic, and the combined datasets, emerging from a quantitative proteogenomic atlas of 15 sweet cherry (<i>Prunus avium</i> L.) cv. ‘Tragana Edessis’ tissues. The algorithm assesses the impact of intervening in the datasets of the causal structures, using various criteria. The results showed that specific tissues exhibited an intense impact on the causal structures that were considered. In addition, the proteogenomic case demonstrated that biologically related tissues that referred to the same organ induced a similar impact on the causal structures considered, as was biologically expected. However, this result was subtler in both the transcriptomic and the proteomic cases. Furthermore, the causal structures based on a single omic analysis were found to be impacted to a larger extent, compared to the proteogenomic case, probably due to the distinctive biological features related to the proteome or the transcriptome. This study showcases the significance and perspective of assessing the causal structure robustness based on omic databases, in conjunction with causal discovery, and reveals advantages when employing a multiomics (proteogenomic) analysis compared to a single-omic (transcriptomic, proteomic) analysis. |
| first_indexed | 2024-03-08T11:09:52Z |
| format | Article |
| id | doaj.art-e59e0898770b40abb0851203a638d905 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-08T11:09:52Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-e59e0898770b40abb0851203a638d9052024-01-26T14:20:52ZengMDPI AGAgronomy2073-43952023-12-01141810.3390/agronomy14010008Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic PerspectiveMaria Ganopoulou0Aliki Xanthopoulou1Michail Michailidis2Lefteris Angelis3Ioannis Ganopoulos4Theodoros Moysiadis5School of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, GreeceInstitute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 57001 Thessaloniki, GreeceLaboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001 Thessaloniki, GreeceSchool of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, GreeceInstitute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 57001 Thessaloniki, GreeceInstitute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 57001 Thessaloniki, GreeceCausal discovery is a highly promising tool with a broad perspective in the field of biology. In this study, a causal structure robustness assessment algorithm is proposed and employed on the causal structures obtained, based on transcriptomic, proteomic, and the combined datasets, emerging from a quantitative proteogenomic atlas of 15 sweet cherry (<i>Prunus avium</i> L.) cv. ‘Tragana Edessis’ tissues. The algorithm assesses the impact of intervening in the datasets of the causal structures, using various criteria. The results showed that specific tissues exhibited an intense impact on the causal structures that were considered. In addition, the proteogenomic case demonstrated that biologically related tissues that referred to the same organ induced a similar impact on the causal structures considered, as was biologically expected. However, this result was subtler in both the transcriptomic and the proteomic cases. Furthermore, the causal structures based on a single omic analysis were found to be impacted to a larger extent, compared to the proteogenomic case, probably due to the distinctive biological features related to the proteome or the transcriptome. This study showcases the significance and perspective of assessing the causal structure robustness based on omic databases, in conjunction with causal discovery, and reveals advantages when employing a multiomics (proteogenomic) analysis compared to a single-omic (transcriptomic, proteomic) analysis.https://www.mdpi.com/2073-4395/14/1/8causalityDAGmultiomicsPC algorithmproteogenomicsweet cherry |
| spellingShingle | Maria Ganopoulou Aliki Xanthopoulou Michail Michailidis Lefteris Angelis Ioannis Ganopoulos Theodoros Moysiadis Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective Agronomy causality DAG multiomics PC algorithm proteogenomic sweet cherry |
| title | Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective |
| title_full | Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective |
| title_fullStr | Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective |
| title_full_unstemmed | Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective |
| title_short | Exploring the Robustness of Causal Structures in Omics Data: A Sweet Cherry Proteogenomic Perspective |
| title_sort | exploring the robustness of causal structures in omics data a sweet cherry proteogenomic perspective |
| topic | causality DAG multiomics PC algorithm proteogenomic sweet cherry |
| url | https://www.mdpi.com/2073-4395/14/1/8 |
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