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

Database: dm6 Primary Table: TFIIB_chipnexus_idr Row Count: 25,888 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	59228	`int(10) unsigned`	range
`chromEnd`	59743	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	820	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.40058	`float`	range
`pValue`	16.8416	`float`	range
`qValue`	14.8133	`float`	range
`peak`	53	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	59228	59743	.	820	.	5.40058	16.8416	14.8133	53
585	chr2L	65735	66104	.	959	.	5.26816	18.3067	16.2551	102
585	chr2L	66705	67146	.	1000	.	11.2795	71.122	68.5752	325
585	chr2L	66705	67146	.	1000	.	6.77265	30.1689	27.9592	92
585	chr2L	66705	67146	.	1000	.	8.78056	46.8148	44.4449	179
585	chr2L	72028	73945	.	1000	.	15.7618	455.886	452.224	1151
585	chr2L	72028	73945	.	1000	.	3.59478	33.711	31.4631	505
585	chr2L	72028	73945	.	1000	.	5.4157	77.4225	74.8357	282
585	chr2L	72028	73945	.	1000	.	5.74757	86.5299	83.8881	224
585	chr2L	72028	73945	.	1000	.	6.39083	104.469	101.729	628

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