Schema for Basal Transcription Factors ChIP-exo - ChIP-exo of Basal Transcription Factors in S2R+ Cells

Database: dm6 Primary Table: gfzf_3x_Baumann2018_peakzilla Row Count: 4,376 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18500	`int(10) unsigned`	range
`chromEnd`	18734	`int(10) unsigned`	range
`name`	peakzilla_1035	`varchar(255)`	values
`score`	27	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	16.76	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.5376	`float`	range
`peak`	117	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18500	18734	peakzilla_1035	27	.	16.76	-1	2.5376	117
585	chr2L	18827	19061	peakzilla_2408	7	.	11.85	-1	1.27819	117
585	chr2L	21666	21900	peakzilla_2519	6	.	4.15	-1	1.25571	117
585	chr2L	73213	73447	peakzilla_2511	7	.	6.32	-1	1.25727	117
585	chr2L	107077	107311	peakzilla_2600	6	.	10.42	-1	1.22695	117
585	chr2L	120482	120716	peakzilla_4042	3	.	3.56	-1	1.15927	117
585	chr2L	120991	121225	peakzilla_2407	7	.	11.86	-1	1.27819	117
585	chr2L	121484	121718	peakzilla_2531	6	.	10.85	-1	1.24949	117
585	chr2L	129109	129343	peakzilla_4649	2	.	2.05	-1	1.13906	117
586	chr2L	131770	132004	peakzilla_1633	14	.	4.9	-1	1.98716	117

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Basal Transcription Factors ChIP-exo (TFChIPexo) Track Description


	Description These tracks show the results of the ChIP-exo analyses of the transcription factors that are associated with the core promoters in S2R+ cells, including the Motif 1 Binding Protein (M1BP) and the GST-containing FLYWCH zinc-finger protein (gfzf). To increase the gfzf signal, an additional gfzf sample was crosslinked with dimethyl adipimidate and ethylene glycol bis(succinimidyl succinate), and then with formaldehyde (gfzf_3xlink). The regions that are enriched in the transcription factors were identified by MACS2, Peakzilla, PeakXus. The log likelihood ratio evidence tracks were produced by MACS2. The ChIP-exo datasets were obtained from the Gene Expression Omnibus database at NCBI under the accession numbers GSE97841 and GSE105009. References Baumann DG, Dai MS, Lu H, Gilmour DS. GFZF, a glutathione S-transferase protein implicated in cell cycle regulation and hybrid inviability, is a transcriptional co-activator. Mol Cell Biol. 2018. Mol Cell Biol 38:e00476-17. Baumann DG, Gilmour DS. A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes. Nucleic Acids Res. 2017 Oct 13;45(18):10481-10491. 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. Hartonen T, Sahu B, Dave K, Kivioja T, Taipale J. PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments. Bioinformatics. 2016 Sep 1;32(17):i629-i638. 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.

Description

References