Schema for TF ChIP-nexus - ChIP-nexus of Basal Transcription Factors in Kc Cells
  Database: dm6    Primary Table: NELFE_chipnexus_peakxus    Row Count: 535,173   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 47517int(10) unsigned
chromEnd 47559int(10) unsigned
name PeakXus_1varchar(255)
score 1000int(10) unsigned
strand .char(1)
signalValue 69float
pValue 307.653float
qValue 307.653float

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValue
585chr2L4751747559PeakXus_11000.69307.653307.653
585chr2L4841148438PeakXus_2102.15.011.896450.60205
585chr2L5927059327PeakXus_31000.963.217381.49551
585chr2L5936859401PeakXus_4452.352.451860.93755
585chr2L5943759476PeakXus_5418.242.551431.00113
585chr2L5958259603PeakXus_6169.122.583541.0247
585chr2L6049060494PeakXus_718.7.012.091280.70902
585chr2L6059660598PeakXus_814.4.031.482010.40336
585chr2L6145661458PeakXus_912.4.051.304360.31177
585chr2L6193861944PeakXus_1020.8.021.701070.48871

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.