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

Database: dm6 Primary Table: CLAMP_SL2_MSL2_RNAi_idr Row Count: 8,296 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5075	`int(10) unsigned`	range
`chromEnd`	6100	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.3035	`float`	range
`pValue`	145.892	`float`	range
`qValue`	137.743	`float`	range
`peak`	789	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5075	6100	.	1000	.	6.3035	145.892	137.743	789
585	chr2L	5075	6100	.	1000	.	3.35415	40.821	38.5119	228
585	chr2L	66712	67492	.	1000	.	3.11885	63.482	60.8194	226
585	chr2L	66712	67492	.	1000	.	3.38251	52.0513	49.5707	612
585	chr2L	72021	72702	.	1000	.	2.7648	54.6905	52.1684	509
585	chr2L	72863	73595	.	1000	.	3.00284	59.0782	56.4878	344
585	chr2L	73688	74391	.	773	.	1.24834	1.60183	0.32405	603
585	chr2L	73688	74391	.	773	.	2.81131	42.9493	40.6088	190
585	chr2L	102195	102452	.	716	.	2.3881	18.427	16.4571	120
585	chr2L	107816	108379	.	1000	.	4.39607	90.6618	87.5012	245

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