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...
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 ...
The samples without prognostic data were excluded from the UCSC Xena database (http://genome.ucsc.edu), and the clinical information of 368 samples was obtained. We used the key word “drug-resistant” to search in the GeneCards (https://www.genecards.org/) database and obtained 1941 ...
Survival analysis was performed using PROGgeneV2 (watson.compbio.iupui.edu/chirayu/proggene/database), and correlation analysis between gene copy number and survival probability was performed using the UCSC Xena database (http://xena.ucsc.edu/). Statistical analysis Data were obtained from at least...
The data of TCGA and GTEx were derived from UCSC Xena Database. RNAseq data and clinical data from 177 pancreatic cancer samples and 171 normal samples were procured for further analyses after classification and screening. Through differential analysis, we discovered that 166 GSTTK genes were incre...
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...
The copy number variation (CNV) information was downloaded from Xena database (http://xena.ucsc.edu/)14. Ultimately, a cohort consisted of 507 patients was included in our investigation and was randomly divided into the training set (355 patients) and testing set (152 patients) at a ratio ...
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...
TCGA curated survival phenotypic data45 were obtained from UCSC Xena. Cases which had both missing overall survival (OS) and progressive-free interval (PFI) outcome data were excluded from survival modeling. TCGA curated drug response clinical data were compiled from Ding et al.14 Our drug ...