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

Database: dm6 Primary Table: TFIIB_chipnexus_macs Row Count: 37,159 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47515	`int(10) unsigned`	range
`chromEnd`	47552	`int(10) unsigned`	range
`name`	TFIIB_macs_peak_1	`varchar(255)`	values
`score`	124	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.95053	`float`	range
`pValue`	14.4627	`float`	range
`qValue`	12.4784	`float`	range
`peak`	14	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47515	47552	TFIIB_macs_peak_1	124	.	4.95053	14.4627	12.4784	14
585	chr2L	59233	59464	TFIIB_macs_peak_2	148	.	5.40058	16.8416	14.8133	48
585	chr2L	59550	59599	TFIIB_macs_peak_3	68	.	3.7504	8.71397	6.86911	38
585	chr2L	64935	64991	TFIIB_macs_peak_4	266	.	6.93155	28.864	26.6686	32
585	chr2L	65306	65361	TFIIB_macs_peak_5	61	.	3.37899	7.92205	6.1058	10
585	chr2L	65818	65985	TFIIB_macs_peak_6	24	.	2.43583	4.04493	2.40449	148
585	chr2L	66749	67104	TFIIB_macs_peak_7a	279	.	6.77265	30.1689	27.9592	48
585	chr2L	66749	67104	TFIIB_macs_peak_7b	444	.	8.78056	46.8148	44.4449	135
585	chr2L	66749	67104	TFIIB_macs_peak_7c	685	.	11.2795	71.122	68.5752	281
585	chr2L	72034	72862	TFIIB_macs_peak_8a	50	.	1.93983	6.86619	5.08458	60

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