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

Database: dm6 Primary Table: M1BP_chipexo_peakzilla Row Count: 4,395 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18494	`int(10) unsigned`	range
`chromEnd`	18754	`int(10) unsigned`	range
`name`	peakzilla_1435	`varchar(255)`	values
`score`	62	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	37.01	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.3098	`float`	range
`peak`	130	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18494	18754	peakzilla_1435	62	.	37.01	-1	2.3098	130
585	chr2L	18805	19065	peakzilla_2153	20	.	12.54	-1	2.37675	130
585	chr2L	21628	21888	peakzilla_2203	17	.	10.73	-1	2.38722	130
586	chr2L	155478	155738	peakzilla_2923	5	.	4.27	-1	2.46852	130
586	chr2L	156001	156261	peakzilla_802	111	.	29.03	-1	2.4318	130
586	chr2L	158855	159115	peakzilla_282	193	.	113.28	-1	1.97881	130
586	chr2L	165294	165554	peakzilla_4416	2	.	2.18	-1	2.60206	130
586	chr2L	203597	203857	peakzilla_3346	4	.	4.83	-1	2.52288	130
586	chr2L	207247	207507	peakzilla_1191	78	.	9.86	-1	2.48149	130
586	chr2L	250960	251220	peakzilla_2707	7	.	4.72	-1	2.4318	130

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