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

Database: dm6 Primary Table: GSE19025_NHS_HSF_peakzilla Row Count: 5,820 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	37443	`int(10) unsigned`	range
`chromEnd`	37653	`int(10) unsigned`	range
`name`	peakzilla_4641	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.04	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.31238	`float`	range
`peak`	105	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	37443	37653	peakzilla_4641	1	.	3.04	-1	0.31238	105
585	chr2L	62458	62668	peakzilla_2971	2	.	3.57	-1	0.32066	105
585	chr2L	73162	73372	peakzilla_148	7	.	19.25	-1	309.653	105
586	chr2L	152974	153184	peakzilla_9707	1	.	2.2	-1	0.31399	105
586	chr2L	157982	158192	peakzilla_1831	2	.	5.72	-1	0.34285	105
586	chr2L	189164	189374	peakzilla_6965	1	.	2.25	-1	0.31229	105
586	chr2L	194290	194500	peakzilla_6104	1	.	2.02	-1	0.31229	105
587	chr2L	284619	284829	peakzilla_6336	1	.	2.36	-1	0.3122	105
587	chr2L	295028	295238	peakzilla_122	9	.	18.77	-1	309.653	105
587	chr2L	295771	295981	peakzilla_876	2	.	7.25	-1	0.45038	105

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.