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

Database: dm6 Primary Table: TFIIA_chipnexus_macs Row Count: 47,969 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	59242	`int(10) unsigned`	range
`chromEnd`	59335	`int(10) unsigned`	range
`name`	TFIIA_macs_peak_1	`varchar(255)`	values
`score`	207	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.74519	`float`	range
`pValue`	22.6114	`float`	range
`qValue`	20.7885	`float`	range
`peak`	26	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	59242	59335	TFIIA_macs_peak_1	207	.	3.74519	22.6114	20.7885	26
585	chr2L	65850	65908	TFIIA_macs_peak_2	96	.	2.74963	11.3413	9.65129	29
585	chr2L	66718	67167	TFIIA_macs_peak_3a	546	.	6.02075	56.6428	54.6195	80
585	chr2L	66718	67167	TFIIA_macs_peak_3b	984	.	8.39112	100.577	98.4023	175
585	chr2L	66718	67167	TFIIA_macs_peak_3c	2877	.	16.4978	290.241	287.707	276
585	chr2L	67248	67312	TFIIA_macs_peak_4	74	.	2.5126	9.09582	7.44921	37
585	chr2L	72087	72193	TFIIA_macs_peak_5a	77	.	1.82536	9.4058	7.75489	19
585	chr2L	72087	72193	TFIIA_macs_peak_5b	239	.	2.53206	25.7534	23.9046	79
585	chr2L	72232	72863	TFIIA_macs_peak_6a	335	.	2.86563	35.5036	33.588	35
585	chr2L	72232	72863	TFIIA_macs_peak_6b	1223	.	5.08703	124.57	122.332	155

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