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

Database: dm6 Primary Table: TAF2_chipnexus_macs Row Count: 79,900 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	48397	`int(10) unsigned`	range
`chromEnd`	48430	`int(10) unsigned`	range
`name`	TAF2_macs_peak_1	`varchar(255)`	values
`score`	111	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.77188	`float`	range
`pValue`	13.1888	`float`	range
`qValue`	11.1447	`float`	range
`peak`	17	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	48397	48430	TAF2_macs_peak_1	111	.	3.77188	13.1888	11.1447	17
585	chr2L	59243	59289	TAF2_macs_peak_2	111	.	3.77188	13.1888	11.1447	21
585	chr2L	66763	66824	TAF2_macs_peak_3	71	.	3.14323	9.07006	7.16306	31
585	chr2L	66870	67110	TAF2_macs_peak_4a	30	.	2.33497	4.65644	3.09049	20
585	chr2L	66870	67110	TAF2_macs_peak_4b	47	.	2.6942	6.48153	4.72714	84
585	chr2L	66870	67110	TAF2_macs_peak_4c	47	.	2.6942	6.48153	4.72714	141
585	chr2L	66870	67110	TAF2_macs_peak_4d	130	.	4.0413	15.1099	13.0183	212
585	chr2L	67273	67308	TAF2_macs_peak_5	38	.	2.51458	5.53972	3.87048	21
585	chr2L	72501	73053	TAF2_macs_peak_6a	212	.	4.11173	23.4547	21.2072	73
585	chr2L	72501	73053	TAF2_macs_peak_6b	1366	.	11.4095	139.71	136.647	153

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