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

Database: dm6 Primary Table: TAF2_chipnexus_peakxus Row Count: 886,857 Data last updated: 2022-10-20

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue
585	chr2L	47518	47552	PeakXus_1	477	.	33	14.4632	11.6412
585	chr2L	48404	48416	PeakXus_2	181	.	13	3.09318	1.47408
585	chr2L	54445	54468	PeakXus_3	58	.	9.02	1.67788	0.64012
585	chr2L	59236	59289	PeakXus_4	1000	.	53	7.47659	5.03745
585	chr2L	59308	59315	PeakXus_5	30	.	6.04	1.37748	0.4864
585	chr2L	59364	59392	PeakXus_6	105	.	19.01	1.85524	0.73929
585	chr2L	59441	59459	PeakXus_7	100	.	11.03	1.58614	0.58807
585	chr2L	59789	59819	PeakXus_8	175	.	15	2.79141	1.28055
585	chr2L	60462	60465	PeakXus_9	13	.	4.03	1.48201	0.54315
585	chr2L	62028	62052	PeakXus_10	168	.	17.03	1.47063	0.53342

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