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

Database: dm6 Primary Table: NELFE_chipnexus_qnexus Row Count: 99,205 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	59267	`int(10) unsigned`	range
`chromEnd`	59291	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	636	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	66	`float`	range
`pValue`	6.44645	`float`	range
`qValue`	4.90033	`float`	range
`peak`	12	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	59267	59291	.	636	.	66	6.44645	4.90033	12
585	chr2L	59310	59334	.	545	.	66	6.44645	4.90048	12
585	chr2L	65826	65850	.	455	.	42	1.12494	-0.251125	12
585	chr2L	65873	65897	.	432	.	48	2.05333	0.624346	12
585	chr2L	66719	66743	.	477	.	45	1.55285	0.147674	12
585	chr2L	66785	66809	.	614	.	96	18.0545	16.37	12
585	chr2L	66869	66893	.	750	.	123	31.9638	30.1878	12
585	chr2L	66924	66948	.	591	.	129	35.4191	33.626	12
585	chr2L	66959	66983	.	682	.	152	49.7242	47.8682	12
585	chr2L	67013	67037	.	818	.	221	100.882	98.8829	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