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Integration of Gene Expression and DNA Methylation Data Across Different Experiments

Yonatan Itai, View ORCID ProfileNimrod Rappoport, View ORCID ProfileRon Shamir
doi: https://doi.org/10.1101/2022.09.21.508920
Yonatan Itai
1Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978 Israel
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Nimrod Rappoport
1Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978 Israel
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Ron Shamir
1Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978 Israel
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  • For correspondence: rshamir@tau.ac.il
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Abstract

Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it.

Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on eleven TCGA cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared to four state-of-the-art integration algorithms. We also demonstrate INTEND’s ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND’s data-driven approach makes it a valuable multi-omic data integration tool.

The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 22, 2022.
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Integration of Gene Expression and DNA Methylation Data Across Different Experiments
Yonatan Itai, Nimrod Rappoport, Ron Shamir
bioRxiv 2022.09.21.508920; doi: https://doi.org/10.1101/2022.09.21.508920
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Integration of Gene Expression and DNA Methylation Data Across Different Experiments
Yonatan Itai, Nimrod Rappoport, Ron Shamir
bioRxiv 2022.09.21.508920; doi: https://doi.org/10.1101/2022.09.21.508920

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