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

Database: dm6 Primary Table: TAF1_chipexo_macs Row Count: 2,954 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	72382	`int(10) unsigned`	range
`chromEnd`	72732	`int(10) unsigned`	range
`name`	TAF1_chipexo_macs_peak_1a	`varchar(255)`	values
`score`	34	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.83361	`float`	range
`pValue`	5.80611	`float`	range
`qValue`	3.47937	`float`	range
`peak`	97	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	72382	72732	TAF1_chipexo_macs_peak_1a	34	.	4.83361	5.80611	3.47937	97
585	chr2L	72382	72732	TAF1_chipexo_macs_peak_1b	123	.	8.59946	14.9606	12.3001	261
585	chr2L	87243	87497	TAF1_chipexo_macs_peak_2	582	.	25.8732	61.4922	58.2756	127
585	chr2L	107996	108308	TAF1_chipexo_macs_peak_3	2105	.	58.2485	214.484	210.575	160
585	chr2L	120336	121113	TAF1_chipexo_macs_peak_4	490	.	19.4522	52.2222	49.0805	251
585	chr2L	121657	121817	TAF1_chipexo_macs_peak_5	487	.	15.6971	51.9388	48.798	71
585	chr2L	129047	129433	TAF1_chipexo_macs_peak_6	10295	.	251.211	1034.86	1029.58	187
586	chr2L	131820	132269	TAF1_chipexo_macs_peak_7	2001	.	65.5131	203.975	200.1	293
586	chr2L	143262	143441	TAF1_chipexo_macs_peak_8	140	.	10.0173	16.7886	14.0741	85
586	chr2L	158926	159338	TAF1_chipexo_macs_peak_9	1266	.	46.303	130.25	126.656	127

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