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p53 Resources

A p53 BAER of the 943 cistrome genes. The size of each word indicates its frequency of overlap across data sets.
A p53 BAER of the 943 cistrome genes. The size of each word indicates its frequency of overlap across data sets.

The transcriptional networks influenced by the p53 tumor suppressor are well-characterized in many organisms. However, a global understanding of requirements for in vivo interactions between the p53 transcription factor and DNA along with transcriptional relationships across human biological systems in response to various p53 activating situations remains limited. Using a common analysis pipeline, we analyzed 41 data sets from genome-wide human ChIP-seq studies of which 16 have associated gene expression data. The resulting extensive analysis, accessible at the p53 BAER hub via the UCSC browser, provides a robust platform to characterize p53 binding throughout the human genome including direct influence on gene expression and underlying mechanisms. Our rigorous approach revealed a large p53 genome-wide cistrome composed of >900 genes directly targeted by p53. Importantly, we identify a core cistrome signature composed of genes appearing in over half the data sets, and we identify signatures that are treatment- and/or cell-specific, demonstrating new functions for p53 in cell biology. Our analysis reveals a broad homeostatic role for human p53 that is relevant to both basic and translational studies.

The p53 universe: signaling pathways of the potential new p53 cistrome target genes.
The p53 universe: signaling pathways of the potential new p53 cistrome target genes.

The human p53 Binding And Expression Resource (BAER) hub, accessible on the UCSC Genome Browser: https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/hub.txt

The p53 ORIO page:
For hierarchical clustering or to look at trends in the p53 ChIP-seq data using the ORIO (Online Resource for Integrative Omics) platform.

p53 cistrome R Shiny application:
This application provides tools to mine, filter, and view p53 Cistrome data in table format, and with hierarchical clustering of the filtered results. Data tables and visualizations are interactive enabling scientists to look for novel patterns in the data. These features use an R-shiny server, which performs statistical manipulations based upon user interaction.

Citation

Nguyen T-A, 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. 2018. Nucleic Acids Research. [Abstract Nguyen T-A, 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. 2018. Nucleic Acids Research.] [Full Text Nguyen T-A, 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. 2018. Nucleic Acids Research.]

Contact

Daniel Menendez, Ph.D.
Daniel Menendez Rendon, Ph.D.
Staff Scientist
Tel 984-287-4105
Fax 919-541-7593
menendez@niehs.nih.gov
P.O. Box 12233
Mail Drop D3-01
Durham, N.C. 27709
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