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

Database: dm6 Primary Table: NELFE_chipnexus_idr Row Count: 28,742 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47513	`int(10) unsigned`	range
`chromEnd`	47582	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	803	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.86038	`float`	range
`pValue`	36.5385	`float`	range
`qValue`	34.494	`float`	range
`peak`	23	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47513	47582	.	803	.	6.86038	36.5385	34.494	23
585	chr2L	59226	59461	.	795	.	2.84216	6.83235	5.11759	162
585	chr2L	59226	59461	.	795	.	5.58631	25.5846	23.6211	47
585	chr2L	65821	65932	.	770	.	3.09146	9.07079	7.30843	65
585	chr2L	66709	67489	.	1000	.	4.19024	17.1908	15.311	93
585	chr2L	66709	67489	.	1000	.	7.81705	52.7874	50.6506	175
585	chr2L	66709	67489	.	1000	.	48.8083	780.052	776.967	370
585	chr2L	66709	67489	.	1000	.	2.30672	5.29146	3.62251	681
585	chr2L	66709	67489	.	1000	.	2.53598	6.92269	5.20642	760
585	chr2L	66709	67489	.	1000	.	3.43315	12.4671	10.6491	586

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