Statements (50)
| Predicate | Object |
|---|---|
| gptkbp:instanceOf |
genomics data type
|
| gptkbp:analyzes |
bioinformatics tools
chromatin interactions |
| gptkbp:depot |
gptkb:ENCODE
gptkb:4D_Nucleome_Data_Portal gptkb:GEO |
| gptkbp:enables |
identification of chromatin loops
identification of compartments identification of topologically associating domains |
| gptkbp:firstDescribed |
gptkb:Lieberman-Aiden_et_al.
|
| gptkbp:firstPublished |
2009
|
| gptkbp:format |
.cool
.hic .mcool |
| https://www.w3.org/2000/01/rdf-schema#label |
Hi-C data
|
| gptkbp:processor |
gptkb:HiC-Pro
gptkb:HiCExplorer HOMER Juicer |
| gptkbp:producedBy |
gptkb:Hi-C_experiment
|
| gptkbp:relatedTo |
gptkb:ChIA-PET_data
ATAC-seq data Capture-C data |
| gptkbp:requires |
sequencing
PCR amplification crosslinking high-throughput sequencing ligation restriction enzyme digestion |
| gptkbp:resolution |
genome size
restriction enzyme choice sequencing depth varies from kilobase to megabase |
| gptkbp:species |
gptkb:Drosophila
gptkb:human gptkb:mouse gptkb:yeast |
| gptkbp:type |
contact matrix
interaction frequency |
| gptkbp:usedFor |
developmental biology
cancer genomics comparative genomics 3D genome organization analysis identifying structural variants studying genome folding |
| gptkbp:usedIn |
gptkb:chromosome_conformation_capture
|
| gptkbp:visualizes |
gptkb:HiGlass
gptkb:Juicebox |
| gptkbp:bfsParent |
gptkb:ENCODE_Project
|
| gptkbp:bfsLayer |
5
|