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

Database: dm6 Primary Table: GSE19025_20HS_HSF_macs Row Count: 452 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73145	`int(10) unsigned`	range
`chromEnd`	73381	`int(10) unsigned`	range
`name`	GSE19025_20HS_HSF_macs_peak_1	`varchar(255)`	values
`score`	152	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.4007	`float`	range
`pValue`	18.7852	`float`	range
`qValue`	15.2449	`float`	range
`peak`	123	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73145	73381	GSE19025_20HS_HSF_macs_peak_1	152	.	6.4007	18.7852	15.2449	123
587	chr2L	295026	295264	GSE19025_20HS_HSF_macs_peak_2	728	.	15.8816	77.4879	72.8983	112
587	chr2L	295398	295639	GSE19025_20HS_HSF_macs_peak_3	330	.	9.81287	36.9638	33.0482	109
588	chr2L	478679	478822	GSE19025_20HS_HSF_macs_peak_4	81	.	4.17014	11.4966	8.15701	67
588	chr2L	490136	490384	GSE19025_20HS_HSF_macs_peak_5	702	.	12.4406	74.8186	70.2803	116
588	chr2L	492471	492633	GSE19025_20HS_HSF_macs_peak_6	74	.	4.09056	10.7468	7.42585	86
588	chr2L	501883	502018	GSE19025_20HS_HSF_macs_peak_7	54	.	3.30693	8.65626	5.411	72
590	chr2L	740136	740323	GSE19025_20HS_HSF_macs_peak_8	317	.	7.05836	35.6683	31.7832	92
595	chr2L	1362361	1362500	GSE19025_20HS_HSF_macs_peak_9	81	.	4.05382	11.5308	8.18299	74
605	chr2L	2748305	2748545	GSE19025_20HS_HSF_macs_peak_10	468	.	10.9787	50.9816	46.8338	111

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.