Schema for hiHMM Models (R5) - hiHMM Chromatin State Tracks (R5) |
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Database: dm6 Primary Table: hiHMM_M1K16_L3 Row Count: 48,221
| field | example | SQL type | info |
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| bin | 585 | smallint(5) unsigned | range |
| chrom | chr2L | varchar(255) | values |
| chromStart | 0 | int(10) unsigned | range |
| chromEnd | 5099 | int(10) unsigned | range |
| name | 17_Unmap | varchar(255) | values |
| score | 0 | int(10) unsigned | range |
| strand | + | char(1) | values |
| thickStart | 0 | int(10) unsigned | range |
| thickEnd | 5099 | int(10) unsigned | range |
| itemRgb | 16777215 | int(10) unsigned | range |
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | itemRgb |
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| 585 | chr2L | 0 | 5099 | 17_Unmap | 0 | + | 0 | 5099 | 255,255,255 |
| 585 | chr2L | 5100 | 11299 | 10_Rep1 | 0 | + | 5100 | 11299 | 154,7,222 |
| 585 | chr2L | 11300 | 13699 | 8_Egn5 | 0 | + | 11300 | 13699 | 0,152,0 |
| 585 | chr2L | 13700 | 15899 | 7_Egn4 | 0 | + | 13700 | 15899 | 0,255,146 |
| 585 | chr2L | 15900 | 17699 | 5_Egn2 | 0 | + | 15900 | 17699 | 145,195,0 |
| 585 | chr2L | 17700 | 18699 | 1_Pro | 0 | + | 17700 | 18699 | 255,0,0 |
| 585 | chr2L | 18700 | 19299 | 2_Enh1 | 0 | + | 18700 | 19299 | 255,92,0 |
| 585 | chr2L | 19300 | 20499 | 5_Egn2 | 0 | + | 19300 | 20499 | 145,195,0 |
| 585 | chr2L | 20500 | 21499 | 1_Pro | 0 | + | 20500 | 21499 | 255,0,0 |
| 585 | chr2L | 21500 | 22699 | 2_Enh1 | 0 | + | 21500 | 22699 | 255,92,0 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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hiHMM Models (R5) (hiHMM_models) Track Description
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Description
This track shows the results of the joint chromatin state segmentation of the
histone modification data for human, D. melanogaster, and C. elegans
using hiHMM. The analysis results
were lifted from the D. melanogaster Release 5 assembly over to the Release 6 assembly.
This analysis classified each genome into 16 chromatin states. The histone enrichment patterns for each
state are shown in Figure 2
of the manuscript by
Ho JWK and colleagues. The properties of each state are summarized in the table below:
| State | Description | Color |
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| 1 | Promoter | |
| 2 | Enhancer 1 | |
| 3 | Enhancer 2 | |
| 4 | Transcription 5' 1 | |
| 5 | Transcription 5' 2 | |
| 6 | Gene, H4K20me1 | |
| 7 | Transcription 3' 1 | |
| 8 | Transcription 3' 2 | |
| 9 | Transcription 3' 3 | |
| 10 | Polycomb repressed 1 | |
| 11 | Polycomb repressed 2 | |
| 12 | Heterochromatin 1 | |
| 13 | Heterochromatin 2 | |
| 14 | Low signal 1 | |
| 15 | Low signal 2 | |
| 16 | Low signal 3 | |
| 17 | Unmappable | |
Credits
The 16-state iHMM models were obtained from the
Comparative modENCODE / ENCODE
web site.
References
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