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

Database: dm6 Primary Table: PolII_chipnexus_macs Row Count: 32,238 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47515	`int(10) unsigned`	range
`chromEnd`	47577	`int(10) unsigned`	range
`name`	PolII_macs_peak_1	`varchar(255)`	values
`score`	324	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.10951	`float`	range
`pValue`	34.4627	`float`	range
`qValue`	32.4535	`float`	range
`peak`	20	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47515	47577	PolII_macs_peak_1	324	.	6.10951	34.4627	32.4535	20
585	chr2L	59254	59325	PolII_macs_peak_2	50	.	2.67814	6.74349	5.02034	18
585	chr2L	64939	64989	PolII_macs_peak_3	94	.	3.35408	11.2093	9.40145	32
585	chr2L	65035	65064	PolII_macs_peak_4	62	.	2.86388	7.97622	6.22606	14
585	chr2L	65227	65368	PolII_macs_peak_5a	71	.	3.01222	8.94776	7.17781	17
585	chr2L	65227	65368	PolII_macs_peak_5b	71	.	2.99969	8.89634	7.12709	90
585	chr2L	65780	65920	PolII_macs_peak_6	420	.	6.8789	44.0916	42.034	59
585	chr2L	66772	66818	PolII_macs_peak_7	93	.	3.24068	11.1503	9.34318	22
585	chr2L	66866	67187	PolII_macs_peak_8a	35	.	2.31371	5.19719	3.52106	14
585	chr2L	66866	67187	PolII_macs_peak_8b	114	.	3.50576	13.2704	11.4347	98

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