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

Database: dm6 Primary Table: TFIIF_chipnexus_idr Row Count: 21,694 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66714	`int(10) unsigned`	range
`chromEnd`	67398	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	9.06922	`float`	range
`pValue`	21.4096	`float`	range
`qValue`	18.8754	`float`	range
`peak`	305	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66714	67398	.	1000	.	9.06922	21.4096	18.8754	305
585	chr2L	66714	67398	.	1000	.	6.15411	11.8717	9.57573	175
585	chr2L	72235	73942	.	1000	.	11.3743	44.5836	41.691	294
585	chr2L	72235	73942	.	1000	.	2.34751	2.93835	1.17617	691
585	chr2L	72235	73942	.	1000	.	2.72979	3.97594	2.0884	15
585	chr2L	72235	73942	.	1000	.	3.14163	5.18828	3.18997	164
585	chr2L	72235	73942	.	1000	.	3.72607	7.12577	5.01697	503
585	chr2L	72235	73942	.	1000	.	4.64351	10.645	8.39204	1630
585	chr2L	72235	73942	.	1000	.	7.25604	22.1997	19.6505	355
585	chr2L	72235	73942	.	1000	.	7.40337	23.0476	20.4811	938

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