Schema for Heat Shock Proteins ChIP-Seq (S2) - ChIP-Seq of Heat Shock Proteins in S2 Cells

Database: dm6 Primary Table: GSE31226_Hsp90_peakzilla Row Count: 20,558 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5820	`int(10) unsigned`	range
`chromEnd`	6008	`int(10) unsigned`	range
`name`	peakzilla_13806	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.15	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.79317	`float`	range
`peak`	94	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5820	6008	peakzilla_13806	2	.	4.15	-1	1.79317	94
585	chr2L	18823	19011	peakzilla_16163	2	.	2.52	-1	1.35556	94
585	chr2L	35582	35770	peakzilla_16354	2	.	4.23	-1	1.31876	94
585	chr2L	65793	65981	peakzilla_8714	4	.	7.48	-1	2.46852	94
585	chr2L	66388	66576	peakzilla_16613	2	.	2.8	-1	1.27819	94
585	chr2L	66878	67066	peakzilla_649	16	.	5.9	-1	2.82391	94
585	chr2L	67227	67415	peakzilla_4440	6	.	5.76	-1	2.5376	94
585	chr2L	67537	67725	peakzilla_21076	1	.	2.54	-1	0.71942	94
585	chr2L	71641	71829	peakzilla_13828	2	.	2.84	-1	1.78516	94
585	chr2L	72045	72233	peakzilla_10112	3	.	4.72	-1	2.31876	94

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

Heat Shock Proteins ChIP-Seq (S2) (hspChIPSeq) Track Description

Description

These tracks show the results of the ChIP-Seq analyses of heat shock proteins from S2 cells. The regions that are enriched in the heat shock proteins 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 following accession numbers:

Accession	Proteins	Reference
GSE31226	Hsp90	Sawarkar R et al., Cell. 2012
GSE19025	HSF, HSF RNAi Knockdown	Guertin MJ et al., PLoS Genet. 2010

References

Sawarkar R, Sievers C, Paro R. Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli. Cell. 2012 May 11;149(4):807-18.

Guertin MJ, Lis JT. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet. 2010 Sep 9;6(9):e1001114.

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.