DOI: 10.5281/zenodo.13351804
title: p53motifDB

description: This Zenodo repository accompanies the manuscript "p53motifDB: integration of genomic information and tumor suppressor p53 binding motifs" and contains raw data tables, a Shiny app (via dockerfile), and a sqlite database that makes up the p53motifDB (p53 motif database). 

The p53motifDB is a compendium of genomic locations in the human hg38 reference genome that contain recognizable DNA sequences that match the binding preferences for the transcription factor p53. Multiple types of genomic, epigenomic, and genome variation data were integrated with these locations in order to let researchers quickly generate hypotheses about novel activities of p53 or validate known behaviors.

Raw data tables

The raw data tables (raw_tables.tar.gz) are divided into the "primary" table, containing p53 motif locations and other biographical information relating to those genomic locations. The "accesory" tables contain additional descriptive or quantitative information that can be queried based on the information in the "primary" table. A description of table schema for the primary table and all accessory tables can be found in Schema_p53motifDB.xlsx. 

Table_1_DataSources_V2.xlsx contains information about all raw and processed data sources that were used in the construction of the p53motifDB. 

Shiny App

The Shiny App is designed to allow rapid filtering, querying, and downloading of the primary and accessory tables. Users can access a web-based version at https://p53motifDB.its.albany.edu. Users can also deploy the Shiny app locally by downloading and extracting p53motifDB_shiny_V2.zip and doing one of of the following:

Option 1: From the extracted folder, run the included Dockerfile to create a Docker image which will deploy to localhost port 3838. 

Option 2: From the shiny_p53motifDB subfolder, run app_rev4.R from R or RStudio. This requires a number of dependencies, which may not be compatible with your current version of R. We highly recommend accessing the Shiny app via the web or through the Dockerfile.  

sqlite Database

Users can perform more complex database queries (beyond those available in the Shiny app) by first downloading sqlite_db.tar.gz. Unpacking this file will reveal the database file p53motifDB.db. This is a sqlite database file containing the same "primary" and "accessory" data from raw_tables.tar.gz and can be used/queried using standard structured query language. The schema of this database including information about each table and the column contents can be examined in the file Schema_p53motifDB.xlsx. 

The gzipped TAR file sqlite_db_R2.zip also contains all of the files and information neccessary to reconstruct the p53motifDB.db via R. Users can source the included R script (database_sqlite_commit.R) or can open, examine, and run via RStudio.  We strongly advise unpacking the TAR file which will produce a folder called sqlite_db  and then running the included R script from within that folder using either source or running line-by-line in RStudio. The result of this script will be p53motifDB.db and an RData object (sqlite_construction.RData) written to the sqlite_db folder. 



If opening and running database_sqlite_commit.R via RStudio, please uncomment line 10 and comment out lines 13 and 14. 

Please also be aware of the minimal package dependencies in R. The included version of p53motifDB.db was created using R (v. 3.4.0) and the following packages (and versions) available via CRAN:

RSQLite (v. 2.3.7), DBI (v. 1.2.3), tidyverse (2.0.0), and utils (v. 4.3.0) packages


 

Credit

The p53motifDB was created by Morgan Sammons, Gaby Baniulyte, and Sawyer Hicks.

Please let us know if you have any questions, comments, or would like additional datasets included in the next version of the p53motifDB by contacting masammons(at)albany.edu

 

This repository is an update to prior Zenodo record 13351805, with DOI https://doi.org/10.5281/zenodo.13351804.