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

Database: dm6 Primary Table: gfzf_3x_Baumann2018_macs Row Count: 2,420 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18519	`int(10) unsigned`	range
`chromEnd`	18714	`int(10) unsigned`	range
`name`	GFZF_3x_Baumann2018_macs_pe...	`varchar(255)`	values
`score`	584	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	23.1561	`float`	range
`pValue`	61.7675	`float`	range
`qValue`	58.4458	`float`	range
`peak`	110	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18519	18714	GFZF_3x_Baumann2018_macs_peak_1	584	.	23.1561	61.7675	58.4458	110
585	chr2L	18863	18995	GFZF_3x_Baumann2018_macs_peak_2	29	.	4.1681	5.43273	2.95736	103
585	chr2L	121023	121164	GFZF_3x_Baumann2018_macs_peak_3	46	.	5.03099	7.25486	4.6981	72
586	chr2L	131794	132103	GFZF_3x_Baumann2018_macs_peak_4	90	.	5.47755	11.7514	9.04776	74
586	chr2L	156001	156236	GFZF_3x_Baumann2018_macs_peak_5	682	.	22.3413	71.6922	68.2899	123
586	chr2L	158839	159142	GFZF_3x_Baumann2018_macs_peak_6	817	.	21.9424	85.2792	81.7648	142
586	chr2L	207281	207513	GFZF_3x_Baumann2018_macs_peak_7	189	.	9.02857	21.8751	18.9854	109
586	chr2L	252287	252443	GFZF_3x_Baumann2018_macs_peak_8	279	.	13.8937	30.9852	27.9736	95
587	chr2L	277171	277617	GFZF_3x_Baumann2018_macs_peak_9a	387	.	15.3646	41.8473	38.7166	146
587	chr2L	277171	277617	GFZF_3x_Baumann2018_macs_peak_9b	147	.	9.26243	17.5814	14.7599	382

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