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

Database: dm6 Primary Table: GSE19025_20HS_HSF_idr Row Count: 272 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	587	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	295014	`int(10) unsigned`	range
`chromEnd`	295303	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	15.8816	`float`	range
`pValue`	77.4879	`float`	range
`qValue`	72.8983	`float`	range
`peak`	124	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
587	chr2L	295014	295303	.	1000	.	15.8816	77.4879	72.8983	124
587	chr2L	295357	295730	.	1000	.	9.81287	36.9638	33.0482	150
588	chr2L	489833	489968	.	658	.	1.87766	2.52342	0	47
588	chr2L	490063	490409	.	919	.	12.4406	74.8186	70.2803	189
588	chr2L	501788	502099	.	661	.	3.30693	8.65626	5.411	166
605	chr2L	2748248	2748635	.	1000	.	10.9787	50.9816	46.8338	168
622	chr2L	4892066	4892361	.	986	.	6.11886	17.2972	13.7852	165
623	chr2L	5009647	5010118	.	1000	.	13.9983	76.2352	71.6695	262
625	chr2L	5288978	5289321	.	713	.	5.98694	16.4291	12.9373	160
630	chr2L	5977667	5977948	.	1000	.	8.48405	46.0674	41.9939	120

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.