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

Database: dm6 Primary Table: gfzf_Baumann2018_macs Row Count: 1,981 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18582	`int(10) unsigned`	range
`chromEnd`	18721	`int(10) unsigned`	range
`name`	GFZF_Baumann2018_macs_peak_1	`varchar(255)`	values
`score`	968	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	40.0258	`float`	range
`pValue`	100.932	`float`	range
`qValue`	96.8443	`float`	range
`peak`	73	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18582	18721	GFZF_Baumann2018_macs_peak_1	968	.	40.0258	100.932	96.8443	73
585	chr2L	21387	21526	GFZF_Baumann2018_macs_peak_2	1194	.	23.5443	123.88	119.449	58
586	chr2L	156056	156199	GFZF_Baumann2018_macs_peak_3	170	.	10.7989	20.1225	17.0462	92
586	chr2L	158869	159056	GFZF_Baumann2018_macs_peak_4	203	.	12.7943	23.5216	20.3757	93
586	chr2L	252340	252480	GFZF_Baumann2018_macs_peak_5	203	.	12.7943	23.5216	20.3757	71
587	chr2L	285735	285845	GFZF_Baumann2018_macs_peak_6	63	.	6.47273	9.23403	6.36867	60
587	chr2L	305675	305980	GFZF_Baumann2018_macs_peak_7a	61	.	6.29939	8.9333	6.10488	43
587	chr2L	305675	305980	GFZF_Baumann2018_macs_peak_7b	291	.	16.711	32.4059	29.1555	218
588	chr2L	414719	415159	GFZF_Baumann2018_macs_peak_8a	453	.	22.5198	48.83	45.3737	78
588	chr2L	414719	415159	GFZF_Baumann2018_macs_peak_8b	116	.	9.39038	14.601	11.6138	338

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