InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia

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• dc.contributor.author Tsagiopoulou, Maria
• dc.contributor.author Pechlivanis, Nikolaos
• dc.contributor.author Maniou, Maria Christina
• dc.contributor.author Psomopoulos, Fotis
• dc.date.accessioned 2022-05-18T10:14:15Z
• dc.date.available 2022-05-18T10:14:15Z
• dc.date.issued 2022
• dc.description.abstract The integration of multi-omics data can greatly facilitate the advancement of research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful multi-omics data integration. Here, we present a robust framework, called InterTADs, for integrating multi-omics data derived from the same sample, and considering the chromatin configuration of the genome, i.e. the topologically associating domains (TADs). Following the integration process, statistical analysis highlights the differences between the groups of interest (normal versus cancer cells) relating to (i) independent and (ii) integrated events through TADs. Finally, enrichment analysis using KEGG database, Gene Ontology and transcription factor binding sites and visualization approaches are available. We applied InterTADs to multi-omics datasets from 135 patients with chronic lymphocytic leukemia (CLL) and found that the integration through TADs resulted in a dramatic reduction of heterogeneity compared to individual events. Significant differences for individual events and on TADs level were identified between patients differing in the somatic hypermutation status of the clonotypic immunoglobulin genes, the core biological stratifier in CLL, attesting to the biomedical relevance of InterTADs. In conclusion, our approach suggests a new perspective towards analyzing multi-omics data, by offering reasonable execution time, biological benchmarking and potentially contributing to pattern discovery through TADs.
• dc.description.sponsorship ‘Hellenic Network for Precision Medicine’ in the framework of the Hellenic Republic – Siemens Settlement Agreement; European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH – CREATE – INNOVATE [GenOptics, project code: T2E1DK-00407]
• dc.format.mimetype application/pdf
• dc.identifier.citation Tsagiopoulou M, Pechlivanis N, Maniou MC, Psomopoulos F. InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia. NAR Genom Bioinform. 2022 Jan 14;4(1):lqab121. DOI:10.1093/nargab/lqab121
• dc.identifier.doi http://dx.doi.org/10.1093/nargab/lqab121
• dc.identifier.issn 2631-9268
• dc.identifier.uri http://hdl.handle.net/10230/53143
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.rights © Maria Tsagiopoulou et al. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.other Leucèmia limfocítica crònica
• dc.title InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion