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

Database: dm6 Primary Table: gcsdi_2cm Row Count: 2,235 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`	29309	`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`	29309	`int(10) unsigned`	range
`itemRgb`	10813478	`int(10) unsigned`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	thickStart	thickEnd	itemRgb
585	chr2L	0	29309	open_1	+	0	29309	165,0,38
585	chr2L	29309	58933	closed_1	+	29309	58933	49,54,149
73	chr2L	58933	252688	open_2	+	58933	252688	165,0,38
73	chr2L	252688	265771	closed_2	+	252688	265771	49,54,149
587	chr2L	265771	305900	open_3	+	265771	305900	165,0,38
73	chr2L	305900	399645	closed_3	+	305900	399645	49,54,149
73	chr2L	399645	581341	open_4	+	399645	581341	165,0,38
589	chr2L	581341	609093	closed_4	+	581341	609093	49,54,149
73	chr2L	609093	808689	closed_5	+	609093	808689	49,54,149
591	chr2L	808689	886313	open_5	+	808689	886313	165,0,38

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.