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

Database: dm6 Primary Table: TAF2_chipnexus_qnexus Row Count: 99,996 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	67067	`int(10) unsigned`	range
`chromEnd`	67081	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	500	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	43	`float`	range
`pValue`	4.62361	`float`	range
`qValue`	2.89096	`float`	range
`peak`	7	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	67067	67081	.	500	.	43	4.62361	2.89096	7
585	chr2L	72517	72531	.	559	.	59	10.7286	8.78254	7
585	chr2L	72570	72584	.	706	.	77	19.746	17.6205	7
585	chr2L	72661	72675	.	853	.	178	96.217	93.4703	7
585	chr2L	72685	72699	.	471	.	118	46.443	44.0124	7
585	chr2L	72714	72728	.	765	.	87	25.552	23.3419	7
585	chr2L	72753	72767	.	706	.	73	17.5733	15.4858	7
585	chr2L	72786	72800	.	588	.	75	18.6484	16.5426	7
585	chr2L	72829	72843	.	676	.	80	21.4333	19.2818	7
585	chr2L	72893	72907	.	324	.	53	8.2011	6.32601	7

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