We also retrieved gene expression RNAseq of 26 healthy human tissue, which corresponds with the tumor tissues of the TCGA database, in the Genotype-tissue expression (GTEx) database, from the UCSC Xena database, except for muscle, adipose, heart, nerve, pituitary, salivary gland, small ...
Methods: Using bioinformatics tools such as The Cancer Genome Atlas (TCGA) and the UCSC Xena database, a comprehensive pan-cancer analysis of CDKN3 was conducted. The inverstigation encompassed the examination of CDKN3 function actoss 33 different kinds of tumors, as well as the exploration of...
The Cancer Genome Atlas (TCGA; https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) and Genotype-Tissue Expression program (GTEx; https://commonfund.nih.gov/GTex) were downloaded using the UCSC Xena browser Data Hub (https://xenabrowser.net/hub/). RNA sequencin...
Abstract 2584: The UCSC Xena system for cancer genomics data visualization and interpretationThe UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize their private functional ... M Goldman,B Craft,J Zhu,... - 《Cancer Research》 被...
The results of this study are based on the data from TCGA database, UCSC Xena database,GTEx database,GEPIA2 database and TIMER database. We thank the authors who provided the data for this study. This study was supported by National Key Clinical Specialty Construction Project (Clinical Pharma...
Clinical data of tumor patients across 33 cancer types were downloaded from UCSC xena database. We used the ‘survfit’ function in survival R package to calculate the Hazard Ratio (HR) of each TRG gene. The overall survival times of patients were used. If TRP genes were with 0 expressions...
SPHK1expression was analyzed using the TCGA melanoma cohort. TCGA genomic and clinical data were downloaded from the UCSC Xena platform (https://xenabrowser.net/). The analysis population consisted of 342 patients with distant metastasis for whom RNAseq and clinical data overlap. No formal sample...
(CNAs) and expression levels ofGPX7were obtained by mining TCGA-LGG-GBM dataset (1153 samples) by using the UCSC Xena Browser (https://xena.ucsc.edu/). The gene expression profile from RNAseq data was indicated as normalized_log2[norm_count + 1] and CNAs status as Log2 (Tumor/...
Public data sources Normalized data from 606 samples, their phenotypes including and clinical pathological characteristics and curated survival data, were downloaded from The Cancer Genome Atlas (TCGA) using the UCSC Xena Functional Genomics Browser32. The downloaded data included the RNA-Seq dataset (...
9.3.1.1.2.3.2.installation of UCSCXenaTools UCSCXenaTools is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Public omics data from UCSC Xena are supported throughmultiple turn-key Xena Hubs, which are a collection of UCSC-ho...