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

Database: dm6 Primary Table: TBP_chipnexus_macs Row Count: 32,832 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47517	`int(10) unsigned`	range
`chromEnd`	47546	`int(10) unsigned`	range
`name`	TBP_macs_peak_1	`varchar(255)`	values
`score`	45	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.57807	`float`	range
`pValue`	6.31936	`float`	range
`qValue`	4.52211	`float`	range
`peak`	13	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47517	47546	TBP_macs_peak_1	45	.	3.57807	6.31936	4.52211	13
585	chr2L	59239	59310	TBP_macs_peak_2	65	.	4.2095	8.44735	6.56462	17
585	chr2L	65871	65918	TBP_macs_peak_3	51	.	3.56125	6.9992	5.17718	8
585	chr2L	66677	67184	TBP_macs_peak_4a	145	.	5.75916	16.6577	14.5559	54
585	chr2L	66677	67184	TBP_macs_peak_4b	1100	.	19.8223	113.053	110.071	211
585	chr2L	66677	67184	TBP_macs_peak_4c	620	.	13.4583	64.7246	62.0426	277
585	chr2L	66677	67184	TBP_macs_peak_4d	705	.	14.6358	73.3034	70.5568	329
585	chr2L	66677	67184	TBP_macs_peak_4e	285	.	8.24638	30.8841	28.5434	402
585	chr2L	67245	67392	TBP_macs_peak_5	106	.	4.66999	12.6667	10.6572	42
585	chr2L	67448	67477	TBP_macs_peak_6	56	.	3.38505	7.48714	5.6436	13

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