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

Database: dm6 Primary Table: PolII_chipnexus_peakxus Row Count: 454,089 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47518	`int(10) unsigned`	range
`chromEnd`	47561	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	68	`float`	range
`pValue`	307.653	`float`	range
`qValue`	307.653	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	47518	47561	PeakXus_1	1000	.	68	307.653	307.653
585	chr2L	59235	59289	PeakXus_2	1000	.	53	6.92298	5.01233
585	chr2L	59323	59327	PeakXus_3	160	.	15	6.20829	4.34359
585	chr2L	59365	59398	PeakXus_4	751	.	37	5.58741	3.7691
585	chr2L	59424	59452	PeakXus_5	192	.	23.02	1.65974	0.5244
585	chr2L	59462	59464	PeakXus_6	23	.	10.05	1.30436	0.3148
585	chr2L	59501	59511	PeakXus_7	125	.	19	8.62821	6.62929
585	chr2L	59542	59567	PeakXus_8	89	.	20.02	1.69279	0.53744
585	chr2L	59575	59587	PeakXus_9	116	.	19.04	1.45506	0.40409
585	chr2L	59790	59793	PeakXus_10	13	.	4.03	1.48201	0.42455

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