Subtracks⇓  Description⇓  Architectural Proteins ChIP-Seq (Kc167) Track Settings
 
ChIP-Seq of Architectural Proteins in Kc167 Cells   (All ChIP Seq Tracks)

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Select subtracks by study and protein:
 All Study GSE32584  GSE39521  GSE39664  GSE62904  GSE80700 
Protein
BEAF-32 
Cap-H2 
CBP 
Chro 
Cp190 
CTCF 
Dref 
fs(1)h 
GAF 
Ibf1 
Ibf2 
l(3)mbt 
Myc 
Nup98 
pita 
pzg 
TfIIIC 
vtd 
ZIPIC 
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List subtracks: only selected/visible    all    (72 of 72 selected)  
 
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 BEAF-32 (Interphase) MACS2  BEAF-32 (Interphase) MACS2 Peaks for Kc167 Cells   Schema 
 
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 BEAF-32 (Interphase) Peakzilla  BEAF-32 (Interphase) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 BEAF-32 (Interphase) logLR  BEAF-32 (Interphase) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 BEAF-32 (Mitosis) MACS2  BEAF-32 (Mitosis) MACS2 Peaks for Kc167 Cells   Schema 
 
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 BEAF-32 (Mitosis) Peakzilla  BEAF-32 (Mitosis) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 BEAF-32 (Mitosis) logLR  BEAF-32 (Mitosis) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Cap-H2 MACS2  Cap-H2 MACS2 Peaks for Kc167 Cells   Schema 
 
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 Cap-H2 Peakzilla  Cap-H2 Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Cap-H2 logLR  Cap-H2 Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 CBP MACS2  CBP MACS2 Peaks for Kc167 Cells   Schema 
 
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 CBP Peakzilla  CBP Peakzilla Peaks for Kc167 Cells   Schema 
 
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 CBP logLR  CBP Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Chro MACS2  Chro MACS2 Peaks for Kc167 Cells   Schema 
 
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 Chro Peakzilla  Chro Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Chro logLR  Chro Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Cp190 (Interphase) MACS2  Cp190 (Interphase) MACS2 Peaks for Kc167 Cells   Schema 
 
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 Cp190 (Interphase) Peakzilla  Cp190 (Interphase) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Cp190 (Interphase) logLR  Cp190 (Interphase) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Cp190 (Mitosis) MACS2  Cp190 (Mitosis) MACS2 Peaks for Kc167 Cells   Schema 
 
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 Cp190 (Mitosis) Peakzilla  Cp190 (Mitosis) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Cp190 (Mitosis) logLR  Cp190 (Mitosis) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 CTCF (Interphase) MACS2  CTCF (Interphase) MACS2 Peaks for Kc167 Cells   Schema 
 
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 CTCF (Interphase) Peakzilla  CTCF (Interphase) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 CTCF (Interphase) logLR  CTCF (Interphase) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 CTCF (Mitosis) MACS2  CTCF (Mitosis) MACS2 Peaks for Kc167 Cells   Schema 
 
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 CTCF (Mitosis) Peakzilla  CTCF (Mitosis) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 CTCF (Mitosis) logLR  CTCF (Mitosis) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Dref (Interphase) MACS2  Dref (Interphase) MACS2 Peaks for Kc167 Cells   Schema 
 
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 Dref (Interphase) Peakzilla  Dref (Interphase) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Dref (Interphase) logLR  Dref (Interphase) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Dref (Mitosis) MACS2  Dref (Mitosis) MACS2 Peaks for Kc167 Cells   Schema 
 
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 Dref (Mitosis) Peakzilla  Dref (Mitosis) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Dref (Mitosis) logLR  Dref (Mitosis) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 fs(1)h MACS2  fs(1)h MACS2 Peaks for Kc167 Cells   Schema 
 
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 fs(1)h Peakzilla  fs(1)h Peakzilla Peaks for Kc167 Cells   Schema 
 
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 fs(1)h logLR  fs(1)h Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 GAF MACS2  GAF MACS2 Peaks for Kc167 Cells   Schema 
 
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 GAF Peakzilla  GAF Peakzilla Peaks for Kc167 Cells   Schema 
 
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 GAF logLR  GAF Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Ibf1 MACS2  Ibf1 MACS2 Peaks for Kc167 Cells   Schema 
 
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 Ibf1 Peakzilla  Ibf1 Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Ibf1 logLR  Ibf1 Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Ibf2 MACS2  Ibf2 MACS2 Peaks for Kc167 Cells   Schema 
 
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 Ibf2 Peakzilla  Ibf2 Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Ibf2 logLR  Ibf2 Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 l(3)mbt MACS2  l(3)mbt MACS2 Peaks for Kc167 Cells   Schema 
 
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 l(3)mbt Peakzilla  l(3)mbt Peakzilla Peaks for Kc167 Cells   Schema 
 
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 l(3)mbt logLR  l(3)mbt Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Myc (Interphase) MACS2  Myc (Interphase) MACS2 Peaks for Kc167 Cells   Schema 
 
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 Myc (Interphase) Peakzilla  Myc (Interphase) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Myc (Interphase) logLR  Myc (Interphase) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Myc (Mitosis) MACS2  Myc (Mitosis) MACS2 Peaks for Kc167 Cells   Schema 
 
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 Myc (Mitosis) Peakzilla  Myc (Mitosis) Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Myc (Mitosis) logLR  Myc (Mitosis) Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 Nup98 MACS2  Nup98 MACS2 Peaks for Kc167 Cells   Schema 
 
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 Nup98 Peakzilla  Nup98 Peakzilla Peaks for Kc167 Cells   Schema 
 
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 Nup98 logLR  Nup98 Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 pita MACS2  pita MACS2 Peaks for Kc167 Cells   Schema 
 
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 pita Peakzilla  pita Peakzilla Peaks for Kc167 Cells   Schema 
 
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 pita logLR  pita Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 pzg MACS2  pzg MACS2 Peaks for Kc167 Cells   Schema 
 
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 pzg Peakzilla  pzg Peakzilla Peaks for Kc167 Cells   Schema 
 
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 pzg logLR  pzg Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 TfIIIC MACS2  TfIIIC MACS2 Peaks for Kc167 Cells   Schema 
 
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 TfIIIC Peakzilla  TfIIIC Peakzilla Peaks for Kc167 Cells   Schema 
 
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 TfIIIC logLR  TfIIIC Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 vtd MACS2  vtd MACS2 Peaks for Kc167 Cells   Schema 
 
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 vtd Peakzilla  vtd Peakzilla Peaks for Kc167 Cells   Schema 
 
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 vtd logLR  vtd Log Likelihood Enrichment for Kc167 Cells   Schema 
 
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 ZIPIC MACS2  ZIPIC MACS2 Peaks for Kc167 Cells   Schema 
 
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 ZIPIC Peakzilla  ZIPIC Peakzilla Peaks for Kc167 Cells   Schema 
 
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 ZIPIC logLR  ZIPIC Log Likelihood Enrichment for Kc167 Cells   Schema 
    72 of 72 selected

Description

These tracks show the results of the ChIP-Seq analyses of architectural proteins (also known as insulators) from Kc167 cells. The regions that are enriched in the architectural proteins were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2.

The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:

AccessionInsulatorsReference
GSE32584BEAF-32, Cp190, CTCFYang J et al., Nat Commun. 2013
GSE39521MycYang J et al., Nat Commun. 2013
GSE39664DrefGurudatta BV et al., Cell Cycle. 2013
GSE62904Cap-H2, CBP, Chro, fs(1)h, l(3)mbt, pzg, TfIIIC, vtdLi L et al., Mol Cell. 2015
GSE80700GAF, Ibf1, Ibf2, Nup98, pita, ZIPICCubeñas-Potts C et al., Nucleic Acids Res. 2017

References

Yang J, Sung E, Donlin-Asp PG, Corces VG. A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins. Nat Commun. 2013;4:1464.

Gurudatta BV, Yang J, Van Bortle K, Donlin-Asp PG, Corces VG. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle. Cell Cycle. 2013 May 15;12(10):1605-15.

Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Ong CT, Cubeñas-Potts C, Hu M, Lei EP, Bosco G, Qin ZS, Corces VG. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell. 2015 Apr 16;58(2):216-31.

Cubeñas-Potts C, Rowley MJ, Lyu X, Li G, Lei EP, Corces VG. Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res. 2017 Feb 28;45(4):1714-1730.

Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13.

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.

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