Other regulatory elements Tracks
Description
This set of data tracks represents a compilation of regulatory elements used in our analysis.
| Non-coding RNA (microRNA, lincRNA, enhancer RNA) |
| G-quadruplex structures |
| CpG Islands |
| p53 perfect 20mer motif |
Methods
Please note: For a full description of the methods used, refer to Nguyen et al. (2018) in the References section below.
microRNA subtrack was defined as miRBase v21
lincRNA, or long intergenic non-coding RNAs, was defined as Human Body Map lincRNA
FANTOM5 enhancers and enhancer RNAs (eRNAs) eRNAs potentially associated with p53 peaks were defined as Andersson et al.’s active enhancers within 5 kb of a peak.
G-quadruplex (G4) structure subtrack was defined as Hansel-Hertsch et al.’s HaCat or NHEK G4 coordinates
CpG Island subtracks – CpG Island track from UCSC’s Regulation superhub
p53 perfect motif subtrack – identifies the 550 p53 perfect motifs with 0-spacer corresponding exactly to the sequence RRRCWWGYYYRRRCWWGYYY in the hg19 genome.
Credit
These data were analyzed by Nguyen et al., at the National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) in Research Triangle Park, North Carolina, USA. Please direct all questions to menendez@niehs.nih.gov.
https://www.niehs.nih.gov/research/resources/databases/p53/index.cfm
References
Nguyen TT, Grimm SA, Bushel PR, Li J, Li Y, Bennett BD, Lavender CA, Ward JM, Fargo DC, Anderson CW, Li L, Resnick MA, Menendez D. Revealing a human p53 universe. Nucleic Acids Res. 2018;46:8153-8167
Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-73.
Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T. et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507, 455-461.
Hänsel-Hertsch, R., Beraldi, D., Lensing, S.V., Marsico, G., Zyner, K., Parry, A., Di Antonio, M., Pike, J., Kimura, H., Narita, M. et al. (2016) G-quadruplex structures mark human regulatory chromatin. Nat. Genet., 48, 1267-1272.
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US Server