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

Database: dm6 Primary Table: CLAMP_Kc_idr Row Count: 14,212 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66349	`int(10) unsigned`	range
`chromEnd`	66598	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	720	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.32894	`float`	range
`pValue`	16.7187	`float`	range
`qValue`	15.0232	`float`	range
`peak`	136	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66349	66598	.	720	.	2.32894	16.7187	15.0232	136
585	chr2L	66694	67500	.	1000	.	4.99324	97.3586	94.3358	620
585	chr2L	66694	67500	.	1000	.	5.48183	124.445	120.388	250
585	chr2L	72183	73563	.	1000	.	3.26308	66.8397	64.5461	977
585	chr2L	72183	73563	.	1000	.	4.34624	101.118	97.973	363
585	chr2L	87326	87513	.	595	.	1.67547	6.43719	4.92743	87
585	chr2L	102201	102442	.	908	.	2.38598	21.9455	20.1837	118
585	chr2L	107802	108375	.	1000	.	4.67431	110.53	107.05	246
585	chr2L	109028	109484	.	864	.	2.18444	22.6873	20.917	285
585	chr2L	114551	114766	.	690	.	1.94625	11.1629	9.55239	103

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