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

Database: dm6 Primary Table: PolII_chipnexus_qnexus Row Count: 98,725 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	65306	`int(10) unsigned`	range
`chromEnd`	65330	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	432	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	48	`float`	range
`pValue`	1.66636	`float`	range
`qValue`	0.44079	`float`	range
`peak`	12	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	65306	65330	.	432	.	48	1.66636	0.44079	12
585	chr2L	65822	65846	.	705	.	101	18.7743	17.2271	12
585	chr2L	65852	65876	.	636	.	90	13.9996	12.4966	12
585	chr2L	66786	66810	.	500	.	53	2.54348	1.27027	12
585	chr2L	66942	66966	.	591	.	84	11.6293	10.1525	12
585	chr2L	66988	67012	.	455	.	141	40.0809	38.4153	12
585	chr2L	67027	67051	.	886	.	303	167.216	165.286	12
585	chr2L	67063	67087	.	909	.	1120	1206.08	1203.6	12
585	chr2L	67099	67123	.	773	.	440	306.182	304.115	12
585	chr2L	67141	67165	.	500	.	152	46.8576	45.1668	12

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