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

Database: dm6 Primary Table: GSE31226_Hsp90_macs Row Count: 25,118 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5605	`int(10) unsigned`	range
`chromEnd`	6003	`int(10) unsigned`	range
`name`	GSE31226_Hsp90_macs_peak_1b	`varchar(255)`	values
`score`	158	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.20258	`float`	range
`pValue`	18.0753	`float`	range
`qValue`	15.8668	`float`	range
`peak`	309	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5605	6003	GSE31226_Hsp90_macs_peak_1b	158	.	4.20258	18.0753	15.8668	309
585	chr2L	5605	6003	GSE31226_Hsp90_macs_peak_1a	62	.	2.51055	8.03104	6.27915	204
585	chr2L	11820	11939	GSE31226_Hsp90_macs_peak_2	55	.	2.71131	7.28109	5.56719	40
585	chr2L	14483	14672	GSE31226_Hsp90_macs_peak_3a	30	.	2.21894	4.5532	3.01583	48
585	chr2L	14483	14672	GSE31226_Hsp90_macs_peak_3b	32	.	2.25579	4.83438	3.27597	164
585	chr2L	18851	18967	GSE31226_Hsp90_macs_peak_4	122	.	3.49136	14.2559	12.2177	67
585	chr2L	21963	22094	GSE31226_Hsp90_macs_peak_5	68	.	2.97168	8.59044	6.80844	54
585	chr2L	35578	35730	GSE31226_Hsp90_macs_peak_6	97	.	3.23657	11.723	9.79744	76
585	chr2L	47377	47472	GSE31226_Hsp90_macs_peak_7	30	.	1.97494	4.59472	3.05349	29
585	chr2L	65813	65945	GSE31226_Hsp90_macs_peak_8	237	.	5.04105	26.3092	23.707	67

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.