An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions
Topologically associated domains (TADs) represent essential units constituting chromatin’s intricate three-dimensional spatial organization. TADs are stably present across cell types and species, and their influence on vital biological processes, such as gene expression, DNA replication, and chromos...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-10-01
|
| Series: | Electronics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-9292/12/19/4154 |
| _version_ | 1797575943372406784 |
|---|---|
| author | Xuemin Zhao Ran Duan Shaowen Yao |
| author_facet | Xuemin Zhao Ran Duan Shaowen Yao |
| author_sort | Xuemin Zhao |
| collection | DOAJ |
| description | Topologically associated domains (TADs) represent essential units constituting chromatin’s intricate three-dimensional spatial organization. TADs are stably present across cell types and species, and their influence on vital biological processes, such as gene expression, DNA replication, and chromosomal translocation, underscores their significance. Accordingly, the identification of TADs within the Hi-C interaction matrix is a key point in three-dimensional genomics. TADs manifest as contiguous blocks along the diagonal of the Hi-C interaction matrix, which are characterized by dense interactions within blocks and sparse interactions between blocks. An optimization method is proposed to enhance Hi-C interaction matrix data using the empirical mode decomposition method, which requires no prior knowledge and adaptively decomposes Hi-C data into a sum of multiple eigenmodal functions via exploiting the inherent characteristics of variations in the input Hi-C data. We identify TADs within the optimized data and compared the results with five commonly used TAD detection methods, namely the Directionality Index (DI), Interaction Isolation (IS), HiCKey, HiCDB, and TopDom. The results demonstrate the universality and efficiency of the proposed method, highlighting its potential as a valuable tool in TAD identification. |
| first_indexed | 2024-03-10T21:45:29Z |
| format | Article |
| id | doaj.art-2bd3b9953f0b4a97bb3f09896d05ca3d |
| institution | Directory Open Access Journal |
| issn | 2079-9292 |
| language | English |
| last_indexed | 2024-03-10T21:45:29Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Electronics |
| spelling | doaj.art-2bd3b9953f0b4a97bb3f09896d05ca3d2023-11-19T14:18:00ZengMDPI AGElectronics2079-92922023-10-011219415410.3390/electronics12194154An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin InteractionsXuemin Zhao0Ran Duan1Shaowen Yao2School of Information Science and Engineering, Yunnan University, Kunming 650500, ChinaSchool of Information Science and Engineering, Yunnan University, Kunming 650500, ChinaEngineering Research Center of Cyberspace, Yunnan University, Kunming 650500, ChinaTopologically associated domains (TADs) represent essential units constituting chromatin’s intricate three-dimensional spatial organization. TADs are stably present across cell types and species, and their influence on vital biological processes, such as gene expression, DNA replication, and chromosomal translocation, underscores their significance. Accordingly, the identification of TADs within the Hi-C interaction matrix is a key point in three-dimensional genomics. TADs manifest as contiguous blocks along the diagonal of the Hi-C interaction matrix, which are characterized by dense interactions within blocks and sparse interactions between blocks. An optimization method is proposed to enhance Hi-C interaction matrix data using the empirical mode decomposition method, which requires no prior knowledge and adaptively decomposes Hi-C data into a sum of multiple eigenmodal functions via exploiting the inherent characteristics of variations in the input Hi-C data. We identify TADs within the optimized data and compared the results with five commonly used TAD detection methods, namely the Directionality Index (DI), Interaction Isolation (IS), HiCKey, HiCDB, and TopDom. The results demonstrate the universality and efficiency of the proposed method, highlighting its potential as a valuable tool in TAD identification.https://www.mdpi.com/2079-9292/12/19/4154Hi-Ctopologically associated domainsempirical mode decomposition |
| spellingShingle | Xuemin Zhao Ran Duan Shaowen Yao An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions Electronics Hi-C topologically associated domains empirical mode decomposition |
| title | An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions |
| title_full | An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions |
| title_fullStr | An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions |
| title_full_unstemmed | An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions |
| title_short | An Empirical Mode Decomposition-Based Method to Identify Topologically Associated Domains from Chromatin Interactions |
| title_sort | empirical mode decomposition based method to identify topologically associated domains from chromatin interactions |
| topic | Hi-C topologically associated domains empirical mode decomposition |
| url | https://www.mdpi.com/2079-9292/12/19/4154 |
| work_keys_str_mv | AT xueminzhao anempiricalmodedecompositionbasedmethodtoidentifytopologicallyassociateddomainsfromchromatininteractions AT randuan anempiricalmodedecompositionbasedmethodtoidentifytopologicallyassociateddomainsfromchromatininteractions AT shaowenyao anempiricalmodedecompositionbasedmethodtoidentifytopologicallyassociateddomainsfromchromatininteractions AT xueminzhao empiricalmodedecompositionbasedmethodtoidentifytopologicallyassociateddomainsfromchromatininteractions AT randuan empiricalmodedecompositionbasedmethodtoidentifytopologicallyassociateddomainsfromchromatininteractions AT shaowenyao empiricalmodedecompositionbasedmethodtoidentifytopologicallyassociateddomainsfromchromatininteractions |