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

Database: dm6 Primary Table: XPB_chipnexus_idr Row Count: 17,312 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73104	`int(10) unsigned`	range
`chromEnd`	73732	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.62588	`float`	range
`pValue`	7.63938	`float`	range
`qValue`	5.20901	`float`	range
`peak`	383	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73104	73732	.	1000	.	3.62588	7.63938	5.20901	383
585	chr2L	73104	73732	.	1000	.	4.92611	13.3553	10.58	239
585	chr2L	73104	73732	.	1000	.	7.59076	27.4978	24.3066	77
585	chr2L	73104	73732	.	1000	.	3.31126	6.40902	4.08636	31
585	chr2L	73104	73732	.	1000	.	2.46204	3.56274	1.69911	529
585	chr2L	73800	73943	.	771	.	4.88401	13.2435	10.4726	102
585	chr2L	85800	85983	.	925	.	2.08968	2.43941	0.90124	31
585	chr2L	85800	85983	.	925	.	5.53633	15.6868	12.8169	112
585	chr2L	87330	87549	.	901	.	4.90072	12.9444	10.1863	87
585	chr2L	87681	87819	.	545	.	2.3431	3.17677	1.38436	36

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