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

Database: dm6 Primary Table: TRF2_chipexo_macs Row Count: 259 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	129195	`int(10) unsigned`	range
`chromEnd`	129382	`int(10) unsigned`	range
`name`	TRF2_chipexo_macs_peak_1	`varchar(255)`	values
`score`	128	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	9.85718	`float`	range
`pValue`	16.7405	`float`	range
`qValue`	12.8169	`float`	range
`peak`	77	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	129195	129382	TRF2_chipexo_macs_peak_1	128	.	9.85718	16.7405	12.8169	77
586	chr2L	158906	159130	TRF2_chipexo_macs_peak_2	359	.	18.7472	40.8986	35.9666	92
587	chr2L	373339	373487	TRF2_chipexo_macs_peak_3	25	.	5.00806	5.78448	2.56293	121
588	chr2L	479640	479802	TRF2_chipexo_macs_peak_4	224	.	12.3075	26.8635	22.4701	86
620	chr2L	4644678	4644840	TRF2_chipexo_macs_peak_5	45	.	5.81625	7.96611	4.58374	68
661	chr2L	9967234	9967395	TRF2_chipexo_macs_peak_6	295	.	14.5934	34.2962	29.561	71
662	chr2L	10200998	10201165	TRF2_chipexo_macs_peak_7	104	.	7.03193	14.2141	10.4284	88
668	chr2L	11004082	11004233	TRF2_chipexo_macs_peak_8	223	.	13.8981	26.7582	22.3674	67
672	chr2L	11446115	11446340	TRF2_chipexo_macs_peak_9a	78	.	7.83672	11.5378	7.88596	66
672	chr2L	11446115	11446340	TRF2_chipexo_macs_peak_9b	64	.	6.82894	9.99513	6.47251	213

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