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

Database: dm6 Primary Table: M1BP_Baumann2018_macs Row Count: 3,701 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18533	`int(10) unsigned`	range
`chromEnd`	18750	`int(10) unsigned`	range
`name`	M1BP_Baumann2018_macs_peak_1	`varchar(255)`	values
`score`	1623	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	59.5142	`float`	range
`pValue`	166.239	`float`	range
`qValue`	162.391	`float`	range
`peak`	103	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18533	18750	M1BP_Baumann2018_macs_peak_1	1623	.	59.5142	166.239	162.391	103
585	chr2L	18856	18977	M1BP_Baumann2018_macs_peak_2	122	.	9.54642	14.8012	12.2039	72
585	chr2L	21377	21509	M1BP_Baumann2018_macs_peak_3	161	.	5.02265	18.8305	16.164	81
586	chr2L	155964	156422	M1BP_Baumann2018_macs_peak_4	1329	.	44.7039	136.647	132.974	168
586	chr2L	158836	159138	M1BP_Baumann2018_macs_peak_5	1128	.	44.5441	116.4	112.855	160
586	chr2L	207258	207486	M1BP_Baumann2018_macs_peak_6	486	.	17.0535	51.6897	48.639	106
586	chr2L	252263	252514	M1BP_Baumann2018_macs_peak_7	1004	.	41.105	103.904	100.449	128
587	chr2L	277176	277642	M1BP_Baumann2018_macs_peak_8a	704	.	16.2513	73.7118	70.4839	127
587	chr2L	277176	277642	M1BP_Baumann2018_macs_peak_8b	314	.	16.552	34.3404	31.466	361
587	chr2L	285649	285905	M1BP_Baumann2018_macs_peak_9	629	.	28.5625	66.0924	62.9136	136

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