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

Database: dm6 Primary Table: M1BP_chipexo_peakxus Row Count: 14,024 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	13857	`int(10) unsigned`	range
`chromEnd`	13866	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	19	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.04	`float`	range
`pValue`	1.3867	`float`	range
`qValue`	0.02862	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	13857	13866	PeakXus_1	19	.	4.04	1.3867	0.02862
585	chr2L	18616	18643	PeakXus_2	1000	.	100	307.653	307.653
585	chr2L	18653	18693	PeakXus_3	196	.	69.03	1.60203	0.16649
585	chr2L	18705	18719	PeakXus_4	55	.	28	5.58919	3.77995
585	chr2L	18747	18751	PeakXus_5	19	.	11.01	2.01016	0.48535
585	chr2L	18886	18916	PeakXus_6	430	.	23	3.60016	1.90494
585	chr2L	18922	18924	PeakXus_7	17	.	7.01	2.21835	0.6615
585	chr2L	18934	18964	PeakXus_8	76	.	24.01	2.0693	0.53486
585	chr2L	21460	21500	PeakXus_9	738	.	34	11.0562	9.0623
585	chr2L	21747	21749	PeakXus_10	36	.	8.04	1.42392	0.05269

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