+This track represents a comprehensive set of human transcription factor binding sites based on +ChIP-seq experiments generated by production groups in the ENCODE Consortium between +February 2011 and November 2018. +The track presents peak calls (regions of enrichment) +generated by the +the ENCODE Transcription Factor ChIP-seq Processing Pipeline. The related +Txn Factor ChIP E3 tracks +(hg19, +hg38) +provide a summary views of this data. +
++ +
+The display for this track shows site location with the point-source of the peak marked with a +colored vertical bar and the level of enrichment at the site indicated by the darkness of the item. +The display can be filtered to higher valued items, using the +Score range: configuration item. +The score values were computed at UCSC based on signal values assigned by the ENCODE +pipeline. +The input signal values were multiplied by a normalization factor calculated as the ratio +of the maximum score value (1000) to the signal value at 1 standard deviation from the mean, +with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to +mean + 1std across the score range, but assigning all above to the maximum score. + +
+Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the +ENCODE Data Coordination Center for generating and processing the datasets used here. +Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the +ENCODE Data Analysis Center (ZLab at UMass Medical Center) for providing the peak datasets, metadata, and guidance +developing this track.
+ + +ENCODE Project Consortium. + +A user's guide to the encyclopedia of DNA elements (ENCODE). +PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585 +
+ +ENCODE Project Consortium. + +An integrated encyclopedia of DNA elements in the human genome. +Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153 +
++Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee +BT et al. + +ENCODE data at the ENCODE portal. +Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. +PMID: 26527727; PMC: PMC4702836 +
++Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, +Alexander R et al. + +Architecture of the human regulatory network derived from ENCODE data. +Nature. 2012 Sep 6;489(7414):91-100. +PMID: 22955619 +
++Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y +et al. + +Sequence features and chromatin structure around the genomic regions bound by 119 human +transcription factors. +Genome Res. 2012 Sep;22(9):1798-812. +PMID: 22955990; PMC: PMC3431495 +
++Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et +al. + +Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE +consortium. +Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. +PMID: 23203885; PMC: PMC3531197 +
+ +Users may freely download, analyze and publish results based on any ENCODE data without +restrictions. +Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. +
+Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE +production laboratory(s) that generated the datasets used, as described in +Citing ENCODE.
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