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

Database: dm6 Primary Table: M1BP_Baumann2018_peakzilla Row Count: 6,086 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18522	`int(10) unsigned`	range
`chromEnd`	18726	`int(10) unsigned`	range
`name`	peakzilla_737	`varchar(255)`	values
`score`	82	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	47.38	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.56864	`float`	range
`peak`	102	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18522	18726	peakzilla_737	82	.	47.38	-1	2.56864	102
585	chr2L	18826	19030	peakzilla_2249	20	.	12.32	-1	2.27572	102
585	chr2L	21345	21549	peakzilla_2361	18	.	2.17	-1	2.29243	102
585	chr2L	21656	21860	peakzilla_3119	9	.	6.09	-1	2.42022	102
585	chr2L	73123	73327	peakzilla_4087	5	.	3.86	-1	2.5376	102
585	chr2L	102269	102473	peakzilla_4498	4	.	3.29	-1	2.56864	102
585	chr2L	107758	107962	peakzilla_4472	4	.	3.33	-1	2.56864	102
585	chr2L	121072	121276	peakzilla_5037	3	.	2.82	-1	2.55284	102
586	chr2L	156024	156228	peakzilla_335	127	.	37.63	-1	2.22915	102
586	chr2L	158899	159103	peakzilla_605	94	.	54.1	-1	2.48149	102

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