TF ChIP-nexus Track Settings
 
ChIP-nexus of Basal Transcription Factors in Kc Cells   (All ChIP Seq Tracks)

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 Configure 		 NELFE IDR  NELFE IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 NELFE logLR  NELFE Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 PolII IDR  PolII IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 PolII logLR  PolII Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 TAF2 IDR  TAF2 IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 TAF2 logLR  TAF2 Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 TBP IDR  TBP IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 TBP logLR  TBP Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 TFIIA IDR  TFIIA IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 TFIIA logLR  TFIIA Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 TFIIB IDR  TFIIB IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 TFIIB logLR  TFIIB Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 TFIIF IDR  TFIIF IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 TFIIF logLR  TFIIF Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Configure 		 XPB IDR  XPB IDR Peaks for Kc167 Cells   Schema 
 
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 Configure 		 XPB logLR  XPB Log Likelihood Enrichment for Kc167 Cells   Schema 
    

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.