生殖细胞肿瘤相关体细胞型恶性肿瘤突变负担、DNA甲基化景观及蛋白质组特征数据集

数据集获取（Figshare）

• 源站标题：Characterizing the mutational burden, DNA methylation landscape and proteome of germ cell tumor-related somatic-type malignancies to identify the tissue-of-origin, mechanisms of therapy resistance and druggable targets
• DOI：10.6084/m9.figshare.24160911.v2
• 发布日期：2023-09-19
• 文件数：11 个
• 文件总体积：32.83 MB
• 源站页面：https://figshare.com/articles/dataset/Characterizing_the_mutational_burden_DNA_methylation_landscape_and_proteome_of_germ_cell_tumor-related_somatic-type_malignancies_to_identify_the_tissue-of-origin_mechanisms_of_therapy_resistance_and_druggable_targets/24160911

命令行下载

curl -L -o "Characterizing the mutational burden, DNA methylation landscape, and proteome of germ cell tumor-related somatictype malignancies to identify the tissue-of-origin, mechanisms of therapy resistance, and druggable targets.pdf" "https://ndownloader.figshare.com/files/42392493"
curl -L -o "Fig. 1.tiff" "https://ndownloader.figshare.com/files/42392496"
curl -L -o "Fig. 2.tiff" "https://ndownloader.figshare.com/files/42392499"
curl -L -o "Fig. 3.tiff" "https://ndownloader.figshare.com/files/42392502"
curl -L -o "Fig. 4.tiff" "https://ndownloader.figshare.com/files/42392505"
curl -L -o "Fig. 5.tiff" "https://ndownloader.figshare.com/files/42392508"
curl -L -o "Fig. S1.tiff" "https://ndownloader.figshare.com/files/42392511"
curl -L -o "Fig. S2.tiff" "https://ndownloader.figshare.com/files/42392520"

文件清单

• Characterizing the mutational burden, DNA methylation landscape, and proteome of germ cell tumor-related somatictype malignancies to identify the tissue-of-origin, mechanisms of therapy resistance, and druggable targets.pdf（2.40 MB）
• Fig. 1.tiff（6.21 MB）
• Fig. 2.tiff（2.67 MB）
• Fig. 3.tiff（2.16 MB）
• Fig. 4.tiff（2.27 MB）
• Fig. 5.tiff（733.39 KB）
• Fig. S1.tiff（5.66 MB）
• Fig. S2.tiff（1.21 MB）
• Fig. S3.tiff（6.30 MB）
• Fig. S4.tiff（3.19 MB）
• Table S1.xlsx（11.41 KB）

文件总体积 32.83 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
Background:
Germ cell tumors (GCT) might undergo transformation into a somatic-type malignancy (STM), resulting in a cell fate switch to tumors usually found in somatic tissues, such as rhabdomyosarcomas or adenocarcinomas. STM is associated with a poor prognosis, but the molecular and epigenetic mechanisms triggering STM are still enigmatic, the tissue-of-origin is under debate and biomarkers are lacking.
Methods:
To address these questions, we characterized a unique cohort of STM tissues on mutational, epigenetic and protein level using modern and high-throughput methods like TSO assays, 850k DNA methylation arrays and mass spectrometry.
Results and Conclusions:
For the first time, we show that based on DNA methylation and proteome data carcinoma-related STM more closely resemble yolk-sac tumors, while sarcoma-related STM resemble teratoma. STM harbor mutations in FGF signaling factors (FGF6/23, FGFR1/4)highlighting the corresponding pathway as a therapeutic target. Furthermore, STM utilize signaling pathways, like AKT, FGF, MAPK, and WNT to mediate molecular functions coping with oxidative stress, toxin transport, DNA helicase activity, apoptosis and the cell cycle. Collectively, these data might explain the high therapy resistance of STM. Finally, we identified putative novel biomarkers secreted by STM, like EFEMP1, MIF, and DNA methylation at specific CpG dinucleotides.
https://www.nature.com/articles/s41416-023-02425-5

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.6084/m9.figshare.24160911.v2（source: https://figshare.com/articles/dataset/Characterizing_the_mutational_burden_DNA_methylation_landscape_and_proteome_of_germ_cell_tumor-related_somatic-type_malignancies_to_identify_the_tissue-of-origin_mechanisms_of_therapy_resistance_and_druggable_targets/24160911）。