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

Database: dm6 Primary Table: CLAMP_SL2_macs Row Count: 12,767 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5072	`int(10) unsigned`	range
`chromEnd`	6076	`int(10) unsigned`	range
`name`	CLAMP_SL2_macs_peak_1a	`varchar(255)`	values
`score`	124	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.59251	`float`	range
`pValue`	14.2158	`float`	range
`qValue`	12.4615	`float`	range
`peak`	227	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5072	6076	CLAMP_SL2_macs_peak_1a	124	.	2.59251	14.2158	12.4615	227
585	chr2L	5072	6076	CLAMP_SL2_macs_peak_1b	1642	.	7.74532	168.026	164.278	788
585	chr2L	35542	35731	CLAMP_SL2_macs_peak_2	123	.	2.38961	14.1145	12.3629	95
585	chr2L	65738	65957	CLAMP_SL2_macs_peak_3	127	.	2.51369	14.4738	12.716	124
585	chr2L	66713	67126	CLAMP_SL2_macs_peak_4	1037	.	5.07983	106.515	103.779	217
585	chr2L	67182	67464	CLAMP_SL2_macs_peak_5	302	.	3.22716	32.2068	30.2192	139
585	chr2L	72046	72786	CLAMP_SL2_macs_peak_6a	163	.	2.27469	18.1491	16.3353	155
585	chr2L	72046	72786	CLAMP_SL2_macs_peak_6b	763	.	3.86269	78.8186	76.3849	484
585	chr2L	72968	73532	CLAMP_SL2_macs_peak_7	784	.	3.86977	80.8552	78.4019	256
585	chr2L	73724	74148	CLAMP_SL2_macs_peak_8	407	.	3.04077	42.8902	40.7928	195

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