ArticleBMC genomics2019
TADKB: Family classification and a knowledge base of topologically associating domains.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
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- Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants.American journal of human genetics · 2026Article
- Single-cell analysis reveals the cellular and transcriptional heterogeneity of the normal pediatric thyroid.Frontiers in endocrinology · 2026Article
- Interplay Between 3D Chromatin Architecture and Gene Regulation at theInternational journal of molecular sciences · 2025Article
- Polymyositis in Kooiker dogs is associated with a 39 kb deletion upstream of the canine IL21/IL2 locus.PLoS genetics · 2025Article
- Noncoding variation near UBE2E2 orchestrates cardiometabolic pathophenotypes through polygenic effectors.JCI insight · 2024Article
- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells.Genome biology · 2024Article
- Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2.Cell genomics · 2024Article
- Learning Micro-C from Hi-C with diffusion models.PLoS computational biology · 2024Article
- Deficiency of lncRNA MERRICAL abrogates macrophage chemotaxis and diabetes-associated atherosclerosis.Cell reports · 2024Article
- Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients.NAR genomics and bioinformatics · 2024Article
- Blood DNA methylation profiling identifies cathepsin Z dysregulation in pulmonary arterial hypertension.Nature communications · 2024Article
- Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR ofbioRxiv : the preprint server for biology · 2023Article
- scHiMe: predicting single-cell DNA methylation levels based on single-cell Hi-C data.Briefings in bioinformatics · 2023Article
- DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.PLoS computational biology · 2023Article
- Technologies, strategies, and cautions when deconvoluting genome-wide association signals: FTO in focus.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2023Review
- G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers.Cancer research · 2023Article
- A Genome-Wide Association Study into the Aetiology of Congenital Solitary Functioning Kidney.Biomedicines · 2022Article
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8 authors.
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Abstract
backgroundTopologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications and detailed information about TADs.
resultsWe built an online knowledge base TADKB integrating knowledge for TADs in eleven cell types of human and mouse. For each TAD, TADKB provides the predicted three-dimensional (3D) structures of chromosomes and TADs, and detailed annotations about the protein-coding genes and long non-coding RNAs (lncRNAs) existent in each TAD. Besides the 3D chromosomal structures inferred by population Hi-C, the single-cell haplotype-resolved chromosomal 3D structures of 17 GM12878 cells are also integrated in TADKB. A user can submit query gene/lncRNA ID/sequence to search for the TAD(s) that contain(s) the query gene or lncRNA. We also classified TADs into families. To achieve that, we used the TM-scores between reconstructed 3D structures of TADs as structural similarities and the Pearson's correlation coefficients between the fold enrichment of chromatin states as functional similarities. All of the TADs in one cell type were clustered based on structural and functional similarities respectively using the spectral clustering algorithm with various predefined numbers of clusters. We have compared the overlapping TADs from structural and functional clusters and found that most of the TADs in the functional clusters with depleted chromatin states are clustered into one or two structural clusters. This novel finding indicates a connection between the 3D structures of TADs and their DNA functions in terms of chromatin states.
conclusionTADKB is available at http://dna.cs.miami.edu/TADKB/ .
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