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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Hodge theory-based biomolecular data analysis |
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Identification Number: |
doi:10.21979/N9/0TK4YR |
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Distributor: |
DR-NTU (Data) |
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Date of Distribution: |
2023-06-23 |
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Version: |
1 |
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Bibliographic Citation: |
Wei, Ronald Koh Joon; Wee, JunJie; Laurent, Valerie Evangelin; Xia, Kelin, 2023, "Replication Data for: Hodge theory-based biomolecular data analysis", https://doi.org/10.21979/N9/0TK4YR, DR-NTU (Data), V1 |
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Citation |
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Title: |
Replication Data for: Hodge theory-based biomolecular data analysis |
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Identification Number: |
doi:10.21979/N9/0TK4YR |
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Authoring Entity: |
Wei, Ronald Koh Joon (Nanyang Technological University) |
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Wee, JunJie (Nanyang Technological University) |
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Laurent, Valerie Evangelin (Nanyang Technological University) |
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Xia, Kelin (Nanyang Technological University) |
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Software used in Production: |
Python |
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Software used in Production: |
MATLAB |
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Grant Number: |
M4081842 |
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Grant Number: |
RG109/19 |
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Grant Number: |
MOE-T2EP20120-0013 |
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Grant Number: |
MOE-T2EP20220-0010 |
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Distributor: |
DR-NTU (Data) |
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Access Authority: |
Xia, Kelin |
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Depositor: |
Wee, JunJie |
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Date of Deposit: |
2023-06-19 |
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Holdings Information: |
https://doi.org/10.21979/N9/0TK4YR |
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Study Scope |
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Keywords: |
Mathematical Sciences, Medicine, Health and Life Sciences, Mathematical Sciences, Medicine, Health and Life Sciences, Hodge theory, Topological associated domain, Chromosomes |
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Abstract: |
Hodge theory reveals the deep intrinsic relations of differential forms and provides a bridge between differential geometry, algebraic topology, and functional analysis. Here we use Hodge Laplacian and Hodge decomposition models to analyze biomolecular structures. Different from traditional graph-based methods, biomolecular structures are represented as simplicial complexes, which can be viewed as a generalization of graph models to their higher-dimensional counterparts. Hodge Laplacian matrices at different dimensions can be generated from the simplicial complex. The spectral information of these matrices can be used to study intrinsic topological information of biomolecular structures. Essentially, the number (or multiplicity) of k-th dimensional zero eigenvalues is equivalent to the k-th Betti number, i.e., the number of k-th dimensional homology groups. The associated eigenvectors indicate the homological generators, i.e., circles or holes within the molecular-based simplicial complex. Furthermore, Hodge decomposition-based HodgeRank model is used to characterize the folding or compactness of the molecular structures, in particular, the topological associated domain (TAD) in high-throughput chromosome conformation capture (Hi-C) data. Mathematically, molecular structures are represented in simplicial complexes with certain edge flows. The HodgeRank-based average/total inconsistency (AI/TI) is used for the quantitative measurements of the folding or compactness of TADs. This is the first quantitative measurement for TAD regions, as far as we know. |
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Kind of Data: |
Raw PDB files and Computational codes |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Identification Number: |
10.1038/s41598-022-12877-z |
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Bibliographic Citation: |
Wei, R. K. J., Wee, J., Laurent, V. E., & Xia, K. (2022). Hodge theory-based biomolecular data analysis. Scientific Reports, 12(1), 9699. |
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Citation |
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Identification Number: |
10356/160448 |
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Bibliographic Citation: |
Wei, R. K. J., Wee, J., Laurent, V. E., & Xia, K. (2022). Hodge theory-based biomolecular data analysis. Scientific Reports, 12(1), 9699. |
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Label: |
Hodge-Theory-main.rar |
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Notes: |
application/x-rar-compressed |