Schema for CLAMP ChIP-Seq - ChIP-Seq for Chromatin-linked Adapter for MSL Proteins (CLAMP)

Database: dm6 Primary Table: CLAMP_SL2_idr Row Count: 8,412 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5053	`int(10) unsigned`	range
`chromEnd`	6087	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.59251	`float`	range
`pValue`	14.2158	`float`	range
`qValue`	12.4615	`float`	range
`peak`	246	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5053	6087	.	1000	.	2.59251	14.2158	12.4615	246
585	chr2L	5053	6087	.	1000	.	7.74532	168.026	164.278	807
585	chr2L	66687	67474	.	1000	.	3.22716	32.2068	30.2192	634
585	chr2L	66687	67474	.	1000	.	5.07983	106.515	103.779	243
585	chr2L	72020	72898	.	993	.	2.27469	18.1491	16.3353	181
585	chr2L	72020	72898	.	993	.	3.86269	78.8186	76.3849	510
585	chr2L	72944	73621	.	1000	.	3.86977	80.8552	78.4019	280
585	chr2L	73701	74181	.	665	.	3.04077	42.8902	40.7928	218
585	chr2L	102197	102478	.	862	.	3.78561	43.9727	41.8647	136
585	chr2L	107768	108381	.	986	.	4.11796	56.8202	54.5927	325

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

CLAMP ChIP-Seq (clamp_chipseq) Track Description


	Description These tracks show the regions in the D. melanogaster genome that are significantly enriched in Chromatin-linked Adapter for MSL Proteins (CLAMP) as determined by MACS2. The signal tracks correspond to the log likelihood enrichment ratios of the treatment versus the DNA input sample as determined by the `bdgcmp` program in MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The CLAMP ChIP-Seq datasets were obtained from the NCBI Gene Expression Omnibus database under the accession number GSE39271. References Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013 Jul 15;27(14):1551-6. 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. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.

Description