Knowledge of the global architecture of the cell nucleus and the spatial organization of genome is critical for understanding gene expression and nuclear function. Single-cell imaging techniques provide a wealth of information on the spatial organization of chromosomes. Computational tools for modelling chromosome structure have broad implications in studying the effect of cell nucleus on higher-order genome organization. Here we describe a multichromosome constrained self-avoiding chromatin model for studying ensembles of genome structural models of budding yeast nucleus. We successfully generated a large number of model genomes of yeast with appropriate chromatin fiber diameter, persistence length, and excluded volume under spatial confinement. By incorporating details of the constraints from single-cell imaging studies, our method can model the budding yeast genome realistically. The model developed here provides a general computational framework for studying the overall architecture of budding yeast genome.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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