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

Database: dm6 Primary Table: TFIIA_chipnexus_qnexus Row Count: 99,734 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66744	`int(10) unsigned`	range
`chromEnd`	66758	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	529	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	59	`float`	range
`pValue`	4.07752	`float`	range
`qValue`	2.55825	`float`	range
`peak`	7	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66744	66758	.	529	.	59	4.07752	2.55825	7
585	chr2L	66772	66786	.	647	.	86	12.8924	11.219	7
585	chr2L	66815	66829	.	676	.	89	14.113	12.4248	7
585	chr2L	66850	66864	.	647	.	105	21.3092	19.5555	7
585	chr2L	66882	66896	.	853	.	162	54.5211	52.5787	7
585	chr2L	66917	66931	.	765	.	150	46.6925	44.7843	7
585	chr2L	66971	66985	.	853	.	196	78.6894	76.6582	7
585	chr2L	67009	67023	.	853	.	278	146.755	144.547	7
585	chr2L	67032	67046	.	618	.	133	36.3144	34.4599	7
585	chr2L	67061	67075	.	618	.	86	12.8924	11.2192	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