基于TCGA的舌鳞状细胞癌ceRNA网络与分子亚型整合基因组分析数据集

数据集获取（Figshare）

• 源站标题：TCGA based integrated genomic analyses of ceRNA network and novel subtypes revealing potential biomarkers for the prognosis and target therapy of tongue squamous cell carcinoma
• DOI：10.1371/journal.pone.0216834
• 发布日期：2019-05-29
• 文件数：8 个
• 文件总体积：189.62 KB
• 源站页面：https://plos.figshare.com/articles/dataset/TCGA_based_integrated_genomic_analyses_of_ceRNA_network_and_novel_subtypes_revealing_potential_biomarkers_for_the_prognosis_and_target_therapy_of_tongue_squamous_cell_carcinoma/8201969

命令行下载

curl -L -o "pone.0216834.s001.docx" "https://ndownloader.figshare.com/files/15285182"
curl -L -o "pone.0216834.s002.docx" "https://ndownloader.figshare.com/files/15285185"
curl -L -o "pone.0216834.s003.docx" "https://ndownloader.figshare.com/files/15285188"
curl -L -o "pone.0216834.s004.docx" "https://ndownloader.figshare.com/files/15285191"
curl -L -o "pone.0216834.s005.docx" "https://ndownloader.figshare.com/files/15285194"
curl -L -o "pone.0216834.s006.docx" "https://ndownloader.figshare.com/files/15285197"
curl -L -o "pone.0216834.s007.docx" "https://ndownloader.figshare.com/files/15285200"
curl -L -o "pone.0216834.s008.docx" "https://ndownloader.figshare.com/files/15285203"

文件清单

• pone.0216834.s001.docx（33.30 KB）
• pone.0216834.s002.docx（20.02 KB）
• pone.0216834.s003.docx（19.65 KB）
• pone.0216834.s004.docx（30.09 KB）
• pone.0216834.s005.docx（28.25 KB）
• pone.0216834.s006.docx（14.97 KB）
• pone.0216834.s007.docx（17.92 KB）
• pone.0216834.s008.docx（25.42 KB）

文件总体积 189.62 KB（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

Objectives
The study aimed to investigate the ceRNA network in biological development of Tongue Squamous Cell Carcinoma (TSCC) and to identify novel molecular subtypes of TSCC to screen potential biomarkers for target therapy and prognosis by using integrated genomic analysis based on The Cancer Genome Atlas (TCGA) database.
Material and methods
Data on gene expressions were downloaded from TCGA and GEO database. Differentially expressed RNAs(DERNAs) were shown by DESeq2 package in R. Functional enrichment analysis of DEmRNAs was performed using clusterprofilers in R. PPI network was established by referring to String website. Survival analysis of DERNAs was carried out by survival package in R. Interactions among mRNAs, miRNAs and lncRNAs were obtained from Starbase v3.0 and used to construct ceRNA network. Consensus Cluster Plus package was applied to identify molecular subtypes. All key genes were validated by comparing them with GEO microarray data. Statistical analyses of clinical features among different subtypes were performed using SPSS 22.0.
Results
A total of 2907 mRNAs (1366 up-regulated and 1541 down-regulated), 191miRNAs (98 up-regulated and 93 down-regulated) and 1831 lncRNAs (1151 up-regulated and 680 down-regulated) were identified from tumor and normal tissues. A ceRNA network was successfully constructed and 15 DEmRNAs, 1 DEmiRNA, 2 DElncRNAs associated with prognosis were employed. Furthermore, we firstly identified 2 molecular subtypes, basal and differentiated, and found that differentiated subtype consumed less alcohol and was related to a better overall survival.
Conclusion
The study constructed a ceRNA network and identified molecular subtypes of TSCC, and our findings provided a novel insight into this intractable cancer and potential therapeutic targets and prognostic indicators.

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.1371/journal.pone.0216834（source: https://plos.figshare.com/articles/dataset/TCGA_based_integrated_genomic_analyses_of_ceRNA_network_and_novel_subtypes_revealing_potential_biomarkers_for_the_prognosis_and_target_therapy_of_tongue_squamous_cell_carcinoma/8201969）。