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

Database: dm6 Primary Table: TAF1_chipexo_peakxus Row Count: 12,767 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	72383	`int(10) unsigned`	range
`chromEnd`	72390	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	38	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.01	`float`	range
`pValue`	2.04183	`float`	range
`qValue`	0.60494	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	72383	72390	PeakXus_1	38	.	6.01	2.04183	0.60494
585	chr2L	72496	72516	PeakXus_2	93	.	10.01	2.13925	0.6797
585	chr2L	72620	72623	PeakXus_3	75	.	9	3.74259	1.9874
585	chr2L	72629	72655	PeakXus_4	349	.	15	4.25462	2.44866
585	chr2L	72685	72694	PeakXus_5	85	.	12	3.36429	1.65703
585	chr2L	87341	87386	PeakXus_6	1000	.	67	307.653	307.653
585	chr2L	87421	87440	PeakXus_7	33	.	29	2.32579	0.81556
585	chr2L	87468	87472	PeakXus_8	23	.	13	2.62009	1.048
585	chr2L	107987	107989	PeakXus_9	45	.	7.01	1.96833	0.55651
585	chr2L	108058	108060	PeakXus_10	108	.	22	3.18498	1.50717

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