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

Database: dm6 Primary Table: TBP_chipnexus_peakxus Row Count: 295,354 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`	47550	`int(10) unsigned`	range
`name`	PeakXus_1	`varchar(255)`	values
`score`	326	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	19	`float`	range
`pValue`	5.79564	`float`	range
`qValue`	3.81273	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	47517	47550	PeakXus_1	326	.	19	5.79564	3.81273
585	chr2L	59234	59274	PeakXus_2	993	.	32	4.50442	2.63538
585	chr2L	59298	59300	PeakXus_3	25	.	6.03	1.48201	0.30231
585	chr2L	59382	59392	PeakXus_4	88	.	10.01	1.97461	0.57641
585	chr2L	59436	59462	PeakXus_5	297	.	13	2.43923	0.89566
585	chr2L	59591	59599	PeakXus_6	19	.	6.02	1.6245	0.35875
585	chr2L	59618	59620	PeakXus_7	31	.	6.01	2.02924	0.60411
585	chr2L	62764	62767	PeakXus_8	13	.	4.03	1.48201	0.30231
585	chr2L	65046	65064	PeakXus_9	103	.	11.02	1.72404	0.41296
585	chr2L	65343	65348	PeakXus_10	45	.	6.02	1.62194	0.35875

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