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

Database: dm6 Primary Table: PolII_chipnexus_idr Row Count: 20,821 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47514	`int(10) unsigned`	range
`chromEnd`	47582	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.10951	`float`	range
`pValue`	34.4627	`float`	range
`qValue`	32.4535	`float`	range
`peak`	21	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47514	47582	.	1000	.	6.10951	34.4627	32.4535	21
585	chr2L	65772	65926	.	1000	.	6.8789	44.0916	42.034	67
585	chr2L	66731	67210	.	1000	.	3.24068	11.1503	9.34318	63
585	chr2L	66731	67210	.	1000	.	70.0768	1386.75	1383.63	347
585	chr2L	72228	72441	.	990	.	4.21228	77.1075	74.9331	33
585	chr2L	72498	72869	.	1000	.	25.9248	1565.93	1562.76	145
585	chr2L	72498	72869	.	1000	.	3.52411	52.5604	50.4678	52
585	chr2L	72498	72869	.	1000	.	4.19111	76.3831	74.2109	238
585	chr2L	73056	73609	.	1000	.	17.4663	888.507	885.577	269
585	chr2L	73056	73609	.	1000	.	28.2018	1771.39	1768.16	126

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