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

Database: dm6 Primary Table: TFIIF_chipnexus_peakxus Row Count: 123,084 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`	47556	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	139	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	14	`float`	range
`pValue`	2.36748	`float`	range
`qValue`	0.63193	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	47517	47556	PeakXus_1	139	.	14	2.36748	0.63193
585	chr2L	59364	59374	PeakXus_2	79	.	6.02	1.65881	0.19781
585	chr2L	59431	59433	PeakXus_3	12	.	6.05	1.30436	0.03915
585	chr2L	65904	65906	PeakXus_4	33	.	5.01	2.1567	0.49322
585	chr2L	66731	66735	PeakXus_5	24	.	7	2.82669	0.98025
585	chr2L	66745	66756	PeakXus_6	89	.	8.01	2.02701	0.40232
585	chr2L	66857	66859	PeakXus_7	42	.	6	2.98863	1.11246
585	chr2L	66884	66898	PeakXus_8	214	.	21	2.32485	0.60378
585	chr2L	66941	66956	PeakXus_9	96	.	21	2.99061	1.11246
585	chr2L	66970	66973	PeakXus_10	54	.	13	4.27312	2.20493

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