Schema for Su(H) ChIP-Seq - ChIP-Seq of Suppressor of Hairless Proteins

Database: dm6 Primary Table: GSE59726_Su_H_goat_ab_peakzilla Row Count: 2,420 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5437	`int(10) unsigned`	range
`chromEnd`	5807	`int(10) unsigned`	range
`name`	peakzilla_8853	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.72	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.12292	`float`	range
`peak`	185	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5437	5807	peakzilla_8853	2	.	2.72	-1	0.12292	185
585	chr2L	90183	90553	peakzilla_8785	4	.	3.82	-1	0.12205	185
586	chr2L	160452	160822	peakzilla_8780	4	.	2.91	-1	0.122	185
586	chr2L	160924	161294	peakzilla_8824	3	.	2.8	-1	0.12257	185
586	chr2L	161419	161789	peakzilla_8790	4	.	2.94	-1	0.12217	185
586	chr2L	161837	162207	peakzilla_8767	5	.	2.49	-1	0.12188	185
586	chr2L	166007	166377	peakzilla_8858	2	.	2.49	-1	0.12297	185
586	chr2L	166291	166661	peakzilla_8860	2	.	2.42	-1	0.12297	185
586	chr2L	166597	166967	peakzilla_8828	3	.	2.39	-1	0.12263	185
586	chr2L	222026	222396	peakzilla_8779	4	.	2.19	-1	0.122	185

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

Su(H) ChIP-Seq (SuHChIPSeq) Track Description


	Description These tracks show the results of the ChIP-Seq analyses of the Suppressor of hairless [Su(H)] protein. The regions that are enriched in the protein were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the accession number GSE59726. References Ozdemir A, Ma L, White KP, Stathopoulos A. Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos. Dev Cell. 2014 Oct 13;31(1):100-13. Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13. 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