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

Database: dm6 Primary Table: GSE19025_20HS_HSF_peakzilla Row Count: 5,375 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47222	`int(10) unsigned`	range
`chromEnd`	47450	`int(10) unsigned`	range
`name`	peakzilla_2811	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.19	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.2008	`float`	range
`peak`	114	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47222	47450	peakzilla_2811	2	.	3.19	-1	0.2008	114
585	chr2L	73161	73389	peakzilla_343	6	.	17.25	-1	2.5376	114
585	chr2L	113331	113559	peakzilla_4742	1	.	2.79	-1	0.21424	114
586	chr2L	162017	162245	peakzilla_4792	1	.	3.37	-1	0.21488	114
587	chr2L	265399	265627	peakzilla_6050	1	.	2.26	-1	0.22279	114
587	chr2L	295015	295243	peakzilla_51	22	.	41.76	-1	309.653	114
587	chr2L	295394	295622	peakzilla_135	13	.	53.38	-1	309.653	114
588	chr2L	412638	412866	peakzilla_7411	1	.	2.02	-1	0.2324	114
588	chr2L	421063	421291	peakzilla_5710	1	.	2.31	-1	0.22055	114
588	chr2L	444658	444886	peakzilla_4518	1	.	2.01	-1	0.21162	114

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.