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

Database: dm6 Primary Table: TBP_chipnexus_idr Row Count: 29,786 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	59233	`int(10) unsigned`	range
`chromEnd`	59462	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	713	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.94665	`float`	range
`pValue`	4.40898	`float`	range
`qValue`	2.71316	`float`	range
`peak`	217	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	59233	59462	.	713	.	2.94665	4.40898	2.71316	217
585	chr2L	66638	67514	.	1000	.	14.6358	73.3034	70.5568	368
585	chr2L	66638	67514	.	1000	.	19.8223	113.053	110.071	250
585	chr2L	66638	67514	.	1000	.	2.36616	3.4797	1.85471	745
585	chr2L	66638	67514	.	1000	.	13.4583	64.7246	62.0426	316
585	chr2L	66638	67514	.	1000	.	4.36545	11.2079	9.23888	646
585	chr2L	66638	67514	.	1000	.	8.24638	30.8841	28.5434	441
585	chr2L	66638	67514	.	1000	.	3.38505	7.48714	5.6436	823
585	chr2L	72048	73943	.	1000	.	4.3067	18.0077	15.8768	258
585	chr2L	72048	73943	.	1000	.	5.45052	27.701	25.4047	1368

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