Scripts for manuscript "Low amplitude copy number gains shape cancer through known and novel oncogenes with associated therapeutic vulnerabilities"

数据集获取（Figshare）

• 源站标题：Scripts for manuscript “Low amplitude copy number gains shape cancer through known and novel oncogenes with associated therapeutic vulnerabilities”
• DOI：10.6084/m9.figshare.28956854.v1
• 发布日期：2025-07-10
• 文件数：27 个
• 文件总体积：172.40 MB
• 源站页面：https://figshare.com/articles/dataset/Scripts_for_manuscript_Low_amplitude_copy_number_gains_shape_cancer_through_known_and_novel_oncogenes_with_associated_therapeutic_vulnerabilities_/28956854

命令行下载

curl -L -o "CCLE_prep.R" "https://ndownloader.figshare.com/files/56095466"
curl -L -o "Figure 1_clean.R" "https://ndownloader.figshare.com/files/56095469"
curl -L -o "Figure 2_clean.R" "https://ndownloader.figshare.com/files/56095472"
curl -L -o "Figure 3_clean.R" "https://ndownloader.figshare.com/files/56095475"
curl -L -o "Figure 4_clean.R" "https://ndownloader.figshare.com/files/56095478"
curl -L -o "Figure 5_clean.R" "https://ndownloader.figshare.com/files/56095481"
curl -L -o "Figure_6_clean.R" "https://ndownloader.figshare.com/files/56095484"
curl -L -o "Functions and packages.R" "https://ndownloader.figshare.com/files/56095487"

文件清单

• CCLE_prep.R（6.13 KB）
• Figure 1_clean.R（10.02 KB）
• Figure 2_clean.R（9.47 KB）
• Figure 3_clean.R（13.41 KB）
• Figure 4_clean.R（6.99 KB）
• Figure 5_clean.R（6.09 KB）
• Figure_6_clean.R（12.17 KB）
• Functions and packages.R（20.58 KB）
• Supplementary Figure 1.R（1.64 KB）
• Supplementary Figure 2.R（3.16 KB）
• Supplementary Figure 3.R（3.88 KB）
• Supplementary Figure 4.R（6.35 KB）
• Supplementary Figure 5.R（782 B）
• Supplementary Figure 6.R（3.32 KB）
• Supplementary Figure 7.R（1.90 KB）
• Supplementary Figure 8.R（1.83 KB）
• Supplementary Figure 9.R（1.11 KB）
• Supplementary Figure 10.R（1.70 KB）
• Supplementary Figure 11.R（2.13 KB）
• intermediate_files.zip（172.26 MB）

文件总体积 172.40 MB（源站 API 实测）。

数据加载示例（图像类）

from PIL import Image
import glob, os

files = (glob.glob(os.path.join(path, "**", "*.png"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.jpg"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.tif"), recursive=True))
print("图像文件数:", len(files))
img = Image.open(files[0]); print("尺寸/模式:", img.size, img.mode)

# torchvision Dataset 方式:
# from torchvision import datasets
# ds = datasets.ImageFolder(path)  # 要求 子目录=类别

目录组织与标注格式以源站说明和下载后实际文件为准。

数据说明

Abstract:
Large chromosomal copy number gains are ubiquitous throughout cancer types. However, which genes drive their selective advantage is not well established, and therefore they are hardly utilized in clinical practice. Our analysis of copy number patterns in pan-cancer datasets suggests that the selective advantage of copy number gains is largely driven by known oncogenes. Analysis of CRISPR screening data identifies a list of 101 genes that are likely to mediate the effect of these gains, which is highly enriched in annotated oncogenes but also contains genes that have not been implicated in cancer so far. Moreover, we show that specific gains are associated with drug sensitivity or resistance, with a strong enrichment of gains of oncogenes with increased sensitivity to inhibitors targeting these specific genes. Finally, we provide examples where gains can function as relevant clinical biomarkers for diagnosis and treatment. Thus, large copy number gains exert their selective advantage through known and novel oncogenes and their systematic analysis could advance precision oncology.

Description
This share contains the R-scripts used to generate the figures and supplementary figures from the mentioned manuscript. All the neccesary packages and custom functions can be found in the Functions and Packages script. Intermediate files and other necessary files can be found in the intermediate_files ZIP file. Source files (segmented CN data, drug screening data, CRISPR screening data etc.) is not included but can be downloaded from the respective sources (Supplementary Table 1).

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.6084/m9.figshare.28956854.v1（source: https://figshare.com/articles/dataset/Scripts_for_manuscript_Low_amplitude_copy_number_gains_shape_cancer_through_known_and_novel_oncogenes_with_associated_therapeutic_vulnerabilities_/28956854）。