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

Database: dm6 Primary Table: M1BP_Baumann2018_peakxus Row Count: 31,020 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	11454	`int(10) unsigned`	range
`chromEnd`	11457	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	29	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.02	`float`	range
`pValue`	1.78241	`float`	range
`qValue`	0.60434	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	11454	11457	PeakXus_1	29	.	4.02	1.78241	0.60434
585	chr2L	18605	18650	PeakXus_2	1000	.	272	307.653	307.653
585	chr2L	18651	18683	PeakXus_3	250	.	130.02	1.70841	0.5414
585	chr2L	18778	18793	PeakXus_4	104	.	11	3.26775	1.74211
585	chr2L	18895	18921	PeakXus_5	1000	.	42	9.04319	7.18576
585	chr2L	18936	18967	PeakXus_6	112	.	32.01	2.07356	0.78635
585	chr2L	19202	19213	PeakXus_7	74	.	7.03	1.50973	0.42887
585	chr2L	21451	21491	PeakXus_8	1000	.	106	307.653	307.653
585	chr2L	21695	21706	PeakXus_9	57	.	10.03	1.55905	0.46028
585	chr2L	21709	21751	PeakXus_10	383	.	19.05	1.3353	0.33832

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