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

Database: dm6 Primary Table: GSE19025_20HS_HSF_KD_peakzilla Row Count: 4,905 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73167	`int(10) unsigned`	range
`chromEnd`	73403	`int(10) unsigned`	range
`name`	peakzilla_155	`varchar(255)`	values
`score`	10	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	30.49	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.19382	`float`	range
`peak`	118	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73167	73403	peakzilla_155	10	.	30.49	-1	2.19382	118
586	chr2L	186446	186682	peakzilla_4894	1	.	2	-1	0.24451	118
586	chr2L	193327	193563	peakzilla_7082	1	.	2.2	-1	0.26106	118
586	chr2L	258084	258320	peakzilla_5179	1	.	2.15	-1	0.24657	118
587	chr2L	269671	269907	peakzilla_741	2	.	4.29	-1	0.25065	118
587	chr2L	295015	295251	peakzilla_208	7	.	13.18	-1	2.02228	118
587	chr2L	376810	377046	peakzilla_3450	2	.	2.09	-1	0.23314	118
588	chr2L	424761	424997	peakzilla_5093	1	.	2.06	-1	0.24603	118
588	chr2L	444245	444481	peakzilla_3841	1	.	2.18	-1	0.23575	118
588	chr2L	452732	452968	peakzilla_2976	2	.	3.48	-1	0.22702	118

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.