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

Database: dm6 Primary Table: TFIIF_chipnexus_macs Row Count: 22,089 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66730	`int(10) unsigned`	range
`chromEnd`	66786	`int(10) unsigned`	range
`name`	TFIIF_macs_peak_1	`varchar(255)`	values
`score`	43	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.21071	`float`	range
`pValue`	6.47676	`float`	range
`qValue`	4.39629	`float`	range
`peak`	38	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66730	66786	TFIIF_macs_peak_1	43	.	4.21071	6.47676	4.39629	38
585	chr2L	66864	67082	TFIIF_macs_peak_2a	95	.	6.15411	11.8717	9.57573	25
585	chr2L	66864	67082	TFIIF_macs_peak_2b	188	.	9.06922	21.4096	18.8754	155
585	chr2L	67274	67331	TFIIF_macs_peak_3	68	.	5.18241	9.05714	6.85911	39
585	chr2L	72388	72410	TFIIF_macs_peak_4	43	.	3.53725	6.46981	4.39629	7
585	chr2L	72497	72679	TFIIF_macs_peak_5a	416	.	11.3743	44.5836	41.691	32
585	chr2L	72497	72679	TFIIF_macs_peak_5b	196	.	7.25604	22.1997	19.6505	93
585	chr2L	72717	72774	TFIIF_macs_peak_6	50	.	3.72607	7.12577	5.01697	21
585	chr2L	72811	72849	TFIIF_macs_peak_7	56	.	3.92057	7.81561	5.67297	31
585	chr2L	73109	73592	TFIIF_macs_peak_8a	204	.	7.40337	23.0476	20.4811	64

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