Schema for TF ChIP-nexus - ChIP-nexus of Basal Transcription Factors in Kc Cells

Database: dm6 Primary Table: XPB_chipnexus_macs Row Count: 20,623 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66798	`int(10) unsigned`	range
`chromEnd`	66829	`int(10) unsigned`	range
`name`	XPB_macs_peak_1	`varchar(255)`	values
`score`	93	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.61994	`float`	range
`pValue`	12.0372	`float`	range
`qValue`	9.32271	`float`	range
`peak`	15	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66798	66829	XPB_macs_peak_1	93	.	5.61994	12.0372	9.32271	15
585	chr2L	72540	72582	XPB_macs_peak_2	26	.	2.88014	4.80796	2.69659	10
585	chr2L	72621	72676	XPB_macs_peak_3	80	.	4.40305	10.6929	8.05193	23
585	chr2L	72802	72847	XPB_macs_peak_4	54	.	3.73514	7.90712	5.45068	21
585	chr2L	73121	73260	XPB_macs_peak_5	243	.	7.59076	27.4978	24.3066	60
585	chr2L	73298	73390	XPB_macs_peak_6	105	.	4.92611	13.3553	10.58	45
585	chr2L	73465	73532	XPB_macs_peak_7	52	.	3.62588	7.63938	5.20901	22
585	chr2L	73811	73935	XPB_macs_peak_8	104	.	4.88401	13.2435	10.4726	91
585	chr2L	78937	79013	XPB_macs_peak_9	34	.	3.2057	5.73676	3.48826	12
585	chr2L	80163	80190	XPB_macs_peak_10	77	.	4.39174	10.3578	7.73417	11

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TF ChIP-nexus (TFChIPnexus) Track Description


	Description These tracks show the results of the ChIP-nexus analyses of transcription factors that are associated with the core promoters. The regions that are enriched in the transcription factors were identified by MACS2, Q-nexus, and PeakXus. The log likelihood ratio evidence tracks were produced by MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The ChIP-nexus datasets were obtained from the Gene Expression Omnibus database at NCBI under the accession number GSE85738. References Shao W, Zeitlinger J. Paused RNA polymerase II inhibits new transcriptional initiation. Nat Genet. 2017 Jul;49(7):1045-1051. Hansen P, Hecht J, Ibn-Salem J, Menkuec BS, Roskosch S, Truss M, Robinson PN. Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus. BMC Genomics. 2016 Nov 4;17(1):873. 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