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

Database: dm6 Primary Table: NELFE_chipnexus_macs Row Count: 30,243 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`	47580	`int(10) unsigned`	range
`name`	NELFE_macs_peak_1	`varchar(255)`	values
`score`	344	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.86038	`float`	range
`pValue`	36.5385	`float`	range
`qValue`	34.494	`float`	range
`peak`	22	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47514	47580	NELFE_macs_peak_1	344	.	6.86038	36.5385	34.494	22
585	chr2L	59233	59401	NELFE_macs_peak_2a	236	.	5.58631	25.5846	23.6211	40
585	chr2L	59233	59401	NELFE_macs_peak_2b	51	.	2.84216	6.83235	5.11759	155
585	chr2L	65831	65905	NELFE_macs_peak_3	73	.	3.09146	9.07079	7.30843	56
585	chr2L	66714	67315	NELFE_macs_peak_4a	153	.	4.19024	17.1908	15.311	88
585	chr2L	66714	67315	NELFE_macs_peak_4b	506	.	7.81705	52.7874	50.6506	170
585	chr2L	66714	67315	NELFE_macs_peak_4c	7769	.	48.8083	780.052	776.967	365
585	chr2L	66714	67315	NELFE_macs_peak_4d	106	.	3.43315	12.4671	10.6491	581
585	chr2L	67374	67404	NELFE_macs_peak_5	36	.	2.30672	5.29146	3.62251	16
585	chr2L	67450	67485	NELFE_macs_peak_6	52	.	2.53598	6.92269	5.20642	19

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