Data Coverage
Data Coverage
Table 1. The summary of entities in GenomicKB
| Entity Type | Entity Sub-type | Data Source | Number of Entities |
|---|---|---|---|
| Coding Elements | Exons | Ensembl | 643060 |
| Genes | Ensembl | 63636 | |
| Transcripts | Ensembl | 236816 | |
| Proteins | Ensembl | 106140 | |
| Epigenomic features | ChromHMM State | ChromHMM | 4143551 |
| DNase-hypersensitivity sites | ENCODE | 21858996 | |
| Transcriptional factor binding site | ENCODE | 219830128 | |
| Transcriptional factor binding motifs | MotifMap | 4473184 | |
| Histone modification site | ENCODE | 44947427 | |
| Replication Timing | 4D Nucleome (4DN) | 354962 | |
| Non-Coding Elements | Enhancers | ENdb | 249 |
| EnhancerAtlas | 2895465 | ||
| Insulators | ENCODE | 72535 | |
| non_coding_RNA | RNAcentral | 474380 | |
| Promoter | The Eukaryotic Promoter Database (EPD) | 21071 | |
| ENCODE | 32650 | ||
| Super-enhancers | dbSuper | 65816 | |
| Ontologies | Tissue and cell lines | NCBO | 35155 |
| Experimental Factor | NCBO | 35469 | |
| Gene ontologies | NCBO | 50726 | |
| 3D structures | AB compartment | 4D Nucleome (4DN) | 7879 |
| Frequently interacting regions (FIRES) | FIRE studies | 73131 | |
| Topological associating domains (TADs) | 4D Nucleome (4DN) | 49856 | |
| Chromatin loops | 4D Nucleome (4DN) | 46906 | |
| Genomic Variants | Sequence variants | dbSNP | 21107464 |
| GWAS Catalog | 12790 | ||
| Structural variants | Database of Genomic Variants (DGV) | 808608 | |
| dbVar | 67718 |
Table 2. The summary of relationships in GenomicKB frontend
| Relationship type | Relationship subtype | From | To |
|---|---|---|---|
| Positional | Overlap (overlap) | All entities that have a location property | All entities that have a location property |
| Locate in (locate_in) | All entities that have a location property | All entities that have a location property | |
| Upstream | All entities that have a location property | All entities that have a location property | |
| Downstream | All entities that have a location property | All entities that have a location property | |
| Expression | Express into | Gene | Transcriptional factor |
| Express in | Gene | Tissue and cell line | |
| Transcribe (transcribe_into) | Gene | Transcript | |
| Translate (translate_into) | Transcript | Protein | |
| Include | Transcript | Exon | |
| Regulatory | Regulate | Gene | Gene |
| Enhancer | Gene | ||
| Expression QTLs (correlate_with) | Variant | Gene | |
| Variant | Ontology | ||
| GWAS association | Sequence variant | Ontology | |
| Interaction | Ligand receptor pair | Gene | Gene |
| Protein Interaction | Gene | Gene | |
| Annotation | Belong to | Gene | Ontology |
| Non coding RNA | Ontology | ||
| Function annotation | Genes | Gene Ontology | |
| Non coding RNA | Gene Ontology |