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

Database: dm6 Primary Table: TAF2_chipnexus_idr Row Count: 33,090 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47517	`int(10) unsigned`	range
`chromEnd`	47553	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	711	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.50246	`float`	range
`pValue`	11.3583	`float`	range
`qValue`	9.36705	`float`	range
`peak`	17	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47517	47553	.	711	.	3.50246	11.3583	9.36705	17
585	chr2L	59235	59392	.	858	.	1.70633	2.08634	1.00527	140
585	chr2L	59235	59392	.	858	.	3.77188	13.1888	11.1447	29
585	chr2L	66750	67181	.	796	.	1.79613	2.39904	1.24144	407
585	chr2L	66750	67181	.	796	.	2.33497	4.65644	3.09049	139
585	chr2L	66750	67181	.	796	.	2.6942	6.48153	4.72714	204
585	chr2L	66750	67181	.	796	.	3.14323	9.07006	7.16306	44
585	chr2L	66750	67181	.	796	.	4.0413	15.1099	13.0183	332
585	chr2L	72483	73942	.	1000	.	1.97842	4.29933	2.78609	1286
585	chr2L	72483	73942	.	1000	.	11.4095	139.71	136.647	171

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