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

Database: dm6 Primary Table: TBP_chipnexus_qnexus Row Count: 99,982 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	65871	`int(10) unsigned`	range
`chromEnd`	65885	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	441	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	26	`float`	range
`pValue`	3.36015	`float`	range
`qValue`	2.06305	`float`	range
`peak`	7	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	65871	65885	.	441	.	26	3.36015	2.06305	7
585	chr2L	66727	66741	.	441	.	42	10.4082	8.87112	7
585	chr2L	66771	66785	.	500	.	41	9.8835	8.3579	7
585	chr2L	66818	66832	.	559	.	83	38.5961	36.6752	7
585	chr2L	66877	66891	.	824	.	138	89.8778	87.6342	7
585	chr2L	66944	66958	.	706	.	112	64.169	62.0611	7
585	chr2L	66975	66989	.	676	.	126	77.7246	75.5407	7
585	chr2L	66995	67009	.	676	.	131	82.7314	80.523	7
585	chr2L	67073	67087	.	559	.	70	28.459	26.6415	7
585	chr2L	67121	67135	.	294	.	27	3.7058	2.39071	7

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