PCaModelSystemRNA contains RNA abundance outputs and statistical results from a variety of prostate cancer (PCa) model systems. Statistical results correspond to various experimental manipulations (e.g. pharmacological treatments, gene perturbations, spatial and temporal variations, etc.) and result from standardized and maintained bioinformatic workflows.
Package includes features for:
- Low-abundance filtering
- Pre-ranked gene set enrichment analysis (GSEA)
- Tools for data visualization (e.g.
create.volcano.plot,create.correlation.heatmapandcluster.stats.heatmap) - Meta-analysis methods for combining P-values
- Interconverting Homo sapiens and Mus musculus ENSEMBL gene-IDs
To install latest version from GitHub:
if (!requireNamespace('devtools', quietly = TRUE)) {
install.packages('devtools');
}
devtools::install_github('uclahs-cds/package-PCaModelSystemRNA');
| Publication Date | Publication (PMID) | GEO Accession | Species | Condition(s) | Sample Number | Biological States | Median Total Reads |
|---|---|---|---|---|---|---|---|
| 2023-10-09 | 37815914 | GSE202885 | Human | V16D cells treated with the ARPI Enzalutamide (or DMSO for the control) for various timepoints (24 hrs, 48 hrs, 96 hrs, 144 hrs, and 2.8 months) | 18 | 1 | 4.0x107 ± 3.7x106 |
| 2023-02-01 | 36725887 | GSE220942 | Human | Knockdown or overexpression of GALNT7 in 22Rv1 or DU145 cell lines respectively | 12 | 2 | 4.0x106 ± 2.5x105 |
| 2022-11-03 | 36408179 | GSE211638 | Human | AR-inducible LNCaP cell lines treated with Doxycline (or DMSO for the controls), and/or various concentrations of DHT. | 18 | 3 | 1.7x107 ± 1.5x106 |
| 2019-08-19 | 31260412 | GSE117305 | Human | LNCaP cell lines and 22Rv1 xenografts transduced with control or Myc-N--expression and either intact or castrated | 32 | 6 | 5.7x107 ± 1.3x107 |
| 2019-08-19 | 31260412 | GSE117305 | Mouse | Castrated PTEN-/- GEMMs transduced with control or Myc-N--expression | 6 | 1 | 5.7x107 ± 1.3x107 |
| 2019-08-09 | 31485472 | GSE128749 | Human | LNCaP and LAPC4 cells treated with synthetic androgen (R1881) | 11 | 2 | 1.0x107 ± 1.4x106 |
| 2019-05-06 | 31061526 | GSE117536 | Human | Knockdown of KMT9 in PC-3M cells | 6 | 1 | 3.6x107 ± 3.2x106 |
| 2018-02-05 | 29437778 | GSE101539 | Human | C4-2b cell lines treated with pharmacological or genetic inhibition of MELK | 28 | 4 | 1.6x106 ± 1.5x106 |
| 2018-02-05 | 29437778 | GSE101539 | Mouse | PTEN-/- GEMM prostatic lobes of various ages and histopathological grade, and TP53-/-RB1-/- prostatic lobes of various ages and histopathological grade | 92 | 11 | 1.6x106 ± 1.5x106 |
| Total | 223 | 31 | Total Reads: 8.3x109 |
Authors: Nicholas Nunley, Jaron Arbet, Nicole Zeltser, Takafumi Yamaguchi, Jee Yun Han, Rupert Hugh-White, Dan Knight, Mohammed Faizal Eeman Mootor, Rachel Dang, Nicholas Wiltsie, Andrew Goldstein, Paul Boutros
PCaModelSystemRNA is licensed under the GNU General Public License version 2. See the file LICENSE.md for the terms of the GNU GPL license.
PCaModelSystemRNA is a datasets package for accessing and interrogating standardized and quality-controlled transcriptomic data from various model system sources.
Copyright (C) 2025 University of California Los Angeles ("Boutros Lab") All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.