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

Database: dm6 Primary Table: gfzf_Baumann2018_peakzilla Row Count: 1,429 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18549	`int(10) unsigned`	range
`chromEnd`	18761	`int(10) unsigned`	range
`name`	peakzilla_260	`varchar(255)`	values
`score`	53	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	30.76	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.11919	`float`	range
`peak`	106	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18549	18761	peakzilla_260	53	.	30.76	-1	2.11919	106
586	chr2L	156045	156257	peakzilla_652	28	.	7.33	-1	1.86646	106
586	chr2L	158859	159071	peakzilla_498	35	.	20.6	-1	1.92445	106
586	chr2L	207261	207473	peakzilla_882	19	.	2.94	-1	1.95078	106
586	chr2L	252314	252526	peakzilla_648	28	.	18.01	-1	1.86328	106
587	chr2L	277204	277416	peakzilla_1249	7	.	6.45	-1	1.98716	106
587	chr2L	285690	285902	peakzilla_1029	13	.	8.43	-1	1.97469	106
587	chr2L	292270	292482	peakzilla_1265	6	.	11.97	-1	1.9914	106
587	chr2L	305799	306011	peakzilla_432	39	.	22.98	-1	2.03621	106
588	chr2L	414691	414903	peakzilla_152	68	.	39.35	-1	1.88606	106

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