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

Database: dm6 Primary Table: M1BP_chipexo_macs Row Count: 2,453 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18506	`int(10) unsigned`	range
`chromEnd`	18993	`int(10) unsigned`	range
`name`	M1BP_chipexo_macs_peak_1a	`varchar(255)`	values
`score`	706	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	29.8241	`float`	range
`pValue`	73.5627	`float`	range
`qValue`	70.643	`float`	range
`peak`	119	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18506	18993	M1BP_chipexo_macs_peak_1a	706	.	29.8241	73.5627	70.643	119
585	chr2L	18506	18993	M1BP_chipexo_macs_peak_1b	146	.	9.95533	17.2031	14.6837	420
586	chr2L	155984	156397	M1BP_chipexo_macs_peak_2	1314	.	44.4514	134.698	131.458	153
586	chr2L	158749	159156	M1BP_chipexo_macs_peak_3	2938	.	90.7699	297.79	293.822	238
586	chr2L	207243	207520	M1BP_chipexo_macs_peak_4	799	.	24.1082	82.9694	79.9961	133
586	chr2L	252179	252565	M1BP_chipexo_macs_peak_5	1539	.	54.1578	157.254	153.911	211
587	chr2L	277174	277721	M1BP_chipexo_macs_peak_6a	1134	.	22.407	116.586	113.435	129
587	chr2L	277174	277721	M1BP_chipexo_macs_peak_6b	578	.	23.9249	60.7187	57.8806	384
587	chr2L	285646	285945	M1BP_chipexo_macs_peak_7	1665	.	57.5065	169.992	166.592	134
587	chr2L	292266	292532	M1BP_chipexo_macs_peak_8	441	.	20.8943	46.8629	44.1087	134

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