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

Database: dm6 Primary Table: TFIIF_chipnexus_qnexus Row Count: 99,947 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	64934	`int(10) unsigned`	range
`chromEnd`	64964	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	180	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	13	`float`	range
`pValue`	0.774568	`float`	range
`qValue`	-0.278001	`float`	range
`peak`	15	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	64934	64964	.	180	.	13	0.774568	-0.278001	15
585	chr2L	66753	66783	.	180	.	19	2.2718	0.929293	15
585	chr2L	66804	66834	.	120	.	13	0.774568	-0.278015	15
585	chr2L	66873	66903	.	240	.	28	5.77204	4.20405	15
585	chr2L	66943	66973	.	240	.	38	11.0082	9.27363	15
585	chr2L	67006	67036	.	400	.	46	15.9925	14.1532	15
585	chr2L	67297	67327	.	160	.	25	4.4601	2.95775	15
585	chr2L	72017	72047	.	160	.	13	0.774568	-0.278034	15
585	chr2L	72051	72081	.	160	.	15	1.18779	0.01302	15
585	chr2L	72083	72113	.	100	.	14	0.969893	-0.148394	15

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