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

Database: dm6 Primary Table: TRF2_chipexo_peakzilla Row Count: 757 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	129155	`int(10) unsigned`	range
`chromEnd`	129429	`int(10) unsigned`	range
`name`	peakzilla_112	`varchar(255)`	values
`score`	19	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	12.26	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.23062	`float`	range
`peak`	137	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	129155	129429	peakzilla_112	19	.	12.26	-1	1.23062	137
586	chr2L	158863	159137	peakzilla_47	38	.	23.36	-1	0.94615	137
586	chr2L	208993	209267	peakzilla_556	4	.	3.55	-1	1.67572	137
588	chr2L	479598	479872	peakzilla_204	11	.	19.3	-1	1.42366	137
588	chr2L	490198	490472	peakzilla_776	2	.	3.47	-1	1.81816	137
588	chr2L	490662	490936	peakzilla_54	33	.	4.74	-1	1	137
588	chr2L	499734	500008	peakzilla_309	8	.	5.35	-1	1.54821	137
588	chr2L	507235	507509	peakzilla_428	5	.	4.9	-1	1.60033	137
588	chr2L	511442	511716	peakzilla_695	2	.	3.74	-1	1.76955	137
588	chr2L	523625	523899	peakzilla_379	6	.	6.19	-1	1.59007	137

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