Schema for TF ChIP-nexus - ChIP-nexus of Basal Transcription Factors in Kc Cells
  Database: dm6    Primary Table: TFIIB_chipnexus_peakxus    Row Count: 514,255   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 47517int(10) unsigned
chromEnd 47555int(10) unsigned
name PeakXus_1varchar(255)
score 1000int(10) unsigned
strand .char(1)
signalValue 44float
pValue 307.653float
qValue 307.653float

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValue
585chr2L4751747555PeakXus_11000.44307.653307.653
585chr2L4840548446PeakXus_2161.12.031.474030.3995
585chr2L5926159267PeakXus_3148.222.394450.90607
585chr2L5927059319PeakXus_41000.678.783856.56265
585chr2L5933959346PeakXus_5178.226.733254.62423
585chr2L5936659371PeakXus_6125.214.480532.56185
585chr2L5937859391PeakXus_7483.267.275725.13313
585chr2L5943959469PeakXus_8467.284.128542.25413
585chr2L5954259571PeakXus_9414.312.372280.89008
585chr2L5957459597PeakXus_10523.264.595292.66318

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.