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

Database: dm6 Primary Table: XPB_chipnexus_peakxus Row Count: 193,625 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`	47554	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	133	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	16	`float`	range
`pValue`	2.3855	`float`	range
`qValue`	0.51274	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	47517	47554	PeakXus_1	133	.	16	2.3855	0.51274
585	chr2L	59589	59602	PeakXus_2	22	.	6.04	1.35804	0.12765
585	chr2L	63013	63018	PeakXus_3	15	.	4.04	1.39561	0.14779
585	chr2L	66796	66828	PeakXus_4	437	.	25	5.381	2.66087
585	chr2L	66870	66894	PeakXus_5	173	.	12.01	2.26196	0.45635
585	chr2L	66960	66962	PeakXus_6	13	.	4.03	1.48201	0.18167
585	chr2L	69438	69443	PeakXus_7	15	.	5.03	1.50577	0.18167
585	chr2L	69461	69478	PeakXus_8	46	.	12.03	1.46638	0.17354
585	chr2L	70458	70465	PeakXus_9	19	.	6.02	1.6469	0.2101
585	chr2L	72011	72013	PeakXus_10	13	.	4.03	1.48201	0.18167

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