Schema for GCSDI Models (R5) - General Chromatin Sensitivity to DNase I Configuration Models (R5)

Database: dm6 Primary Table: gcsdi_3cm Row Count: 26,328 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	6029	`int(10) unsigned`	range
`name`	open_1	`varchar(255)`	values
`score`	0	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	0	`int(10) unsigned`	range
`thickEnd`	6029	`int(10) unsigned`	range
`itemRgb`	10813478	`int(10) unsigned`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	thickStart	thickEnd	itemRgb
585	chr2L	0	6029	open_1	+	0	6029	165,0,38
585	chr2L	6029	8616	open_2	+	6029	8616	165,0,38
585	chr2L	8616	9370	open_3	+	8616	9370	165,0,38
585	chr2L	9370	14868	open_4	+	9370	14868	165,0,38
585	chr2L	14868	17550	open_5	+	14868	17550	165,0,38
585	chr2L	17550	19199	open_6	+	17550	19199	165,0,38
585	chr2L	19199	20365	open_7	+	19199	20365	165,0,38
585	chr2L	20365	21990	open_8	+	20365	21990	165,0,38
585	chr2L	21990	37546	neutral_1	+	21990	37546	186,186,186
585	chr2L	37546	37937	closed_1	+	37546	37937	49,54,149

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GCSDI Models (R5) (GCSDIprofile) Track Description

Description

These tracks show the General Chromatin Sensitivity to DNase I (GCSDI) Configuration Models produced by Milon and colleagues. The colors correspond to the states in the Two-Configuration Model (2CM) and Three-Configuration Model (3CM):

Color	Description
	Open
	Neutral
	Closed

References

Milon B, Sun Y, Chang W, Creasy T, Mahurkar A, Shetty A, Nurminsky D, Nurminskaya M. Map of open and closed chromatin domains in Drosophila genome. BMC Genomics. 2014 Nov 18;15:988. doi: 10.1186/1471-2164-15-988.