Schema for TF ChIP-nexus - ChIP-nexus of Basal Transcription Factors in Kc Cells
  Database: dm6    Primary Table: TFIIA_chipnexus_peakxus    Row Count: 1,174,815   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 47517int(10) unsigned
chromEnd 47556int(10) unsigned
name PeakXus_1varchar(255)
score 1000int(10) unsigned
strand .char(1)
signalValue 50float
pValue 307.653float
qValue 307.653float

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValue
585chr2L4751747556PeakXus_11000.50307.653307.653
585chr2L4840448421PeakXus_2481.2211.17528.86189
585chr2L5927459329PeakXus_3585.72.012.199071.04454
585chr2L5936659401PeakXus_4234.23.012.001840.91675
585chr2L5950659509PeakXus_525.83.250771.76301
585chr2L5962459626PeakXus_625.6.031.482010.60536
585chr2L6009760100PeakXus_718.7.011.968330.90425
585chr2L6018060182PeakXus_825.4.031.482010.60536
585chr2L6145861460PeakXus_912.4.051.304360.49429
585chr2L6152161524PeakXus_1013.4.031.482010.60536

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.