Schema for GAF KD Differential Regions - GAF vs. GAF

Schema for GAF KD Differential Regions - GAF vs. GAF_KD Differential Regions

Database: dm6 Primary Table: GAF_unique Row Count: 5,102 Data last updated: 2022-10-20

field	example	SQL type	info
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	129	`int(10) unsigned`	range
`chromEnd`	2907	`int(10) unsigned`	range
`name`	GAF_unique_1	`varchar(255)`	values
`id`	GAF_unique_1	`varchar(255)`	values
`description`	LLR: 10.45063	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	id	description
chr2L	129	2907	GAF_unique_1	GAF_unique_1	LLR: 10.45063
chr2L	3024	3384	GAF_unique_2	GAF_unique_2	LLR: 6.08889
chr2L	3502	3736	GAF_unique_3	GAF_unique_3	LLR: 5.62296
chr2L	3909	4280	GAF_unique_4	GAF_unique_4	LLR: 9.71878
chr2L	4419	4794	GAF_unique_5	GAF_unique_5	LLR: 26.45369
chr2L	4914	5183	GAF_unique_6	GAF_unique_6	LLR: 5.54272
chr2L	66386	67548	GAF_unique_7	GAF_unique_7	LLR: 20.03521
chr2L	72322	72823	GAF_unique_8	GAF_unique_8	LLR: 18.41055
chr2L	73655	73911	GAF_unique_9	GAF_unique_9	LLR: 7.16008
chr2L	107727	108362	GAF_unique_10	GAF_unique_10	LLR: 11.91960

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

GAF KD Differential Regions (GAF_KD_bdgdiff) Track Description


	Description These tracks show the differential enrichment regions between the GAF and GAF-KD samples as identified by the bdgdiff program in MACS2. The ChIP-Seq dataset was obtained from the Gene Expression Omnibus database at NCBI under the accession number GSE40646 Credits Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet. 2015 Mar 27;11(3):e1005108. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Description