...). Methods: FOXD1 expression was analyzed in The Cancer Genome Atlas (TCGA) pan-cancer data. The clinical prognosis influence of FOXD1 was evaluated by clinical survival data of TCGA. Enrichment analysis of FOXD1 was performed using R packages ‘clusterProfiler’. We downloaded the immune cell infiltration...

...Qiangqiang Zheng; Shihui Min; Qinghua Zhou Accumulating evidence has demonstrated that gene alterations play a crucial role in LUAD development, progression, and prognosis. The present study aimed to identify the hub genes associated with LUAD. In the present study, we used TCGA database to screen...

... This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . ceRNA network Esophageal cancer Immune infiltration Prognostic model TCGA Esophageal cancer (ESCA) is one...

... (TCGA) and International Cancer Genome Consortium (ICGC), which were used as training and validation cohorts, respectively. A prediction model was constructed using univariate Cox regression and Least Absolute Shrinkage and Selection Operator (LASSO) analysis. Patients were divided into high- and low...

... (TCGA) was constructed to further validate the model. Results: Four SR-CDMGs were identified and used to build the predictive model. The risk score of this model was calculated as follows: risk score = (0.01489826 × methylation level of WDR69 ) + (0.15868618 × methylation level of HOXB4 ) + (0.16674959...

... to finding solutions for the prognosis of HCC from the perspective of autophagy. We used a cohort in The Cancer Genome Atlas (TCGA) to evaluate the expression of autophagy-related genes in 371 HCC samples using univariate Cox and lasso Cox regression analysis, and the prognostic features were identified...

... of HCC raw data were downloaded from The Cancer Genome Atlas (TCGA) database. The Wilcoxon signed-rank test, Kruskal–Wallis test and logistic regression were applied to investigate the relevance between the CDK5R1 expression and clinicopathologic characteristics in HCC. Kaplan–Meier and Cox regression...

... to distinguish EVs derived from tumor tissue and normal tissue. Therefore, the prognostic value of tumor-specific EVs was evaluated through related molecules in pancreatic tumor tissue. NA sequencing data of pancreatic adenocarcinoma (PAAD) were acquired from The Cancer Genome Atlas (TCGA) and International...

... in COAD and conduct a prognosis model for clinical utility. Gene expression data of COAD were downloaded from The Cancer Genome Atlas (TCGA), screening and analyzing differentially expressed IGs by bioinformatics. Core genes were screened by univariate and multivariate Cox regression analyses. Survival...

.... In the present study, we aimed to establish and validate a miRNA signature to predict TMB level in endometrial cancer using The Cancer Genome Atlas (TCGA) database. MiRNA expression and somatic mutation profiles of uterine corpus endometrial carcinoma (UCEC) were downloaded from TCGA database. Total 518 patients...

... ( songjukun@163.com ) bioinformatics immune-related gene prognosis stomach adenocarcinoma TCGA Stomach adenocarcinoma (STAD) is the fifth most common malignancy in the world. It is characterized by high mortality, high degree of malignancy, and strong heterogeneity [ 1 ]. In China, more than...

... prognosis and potential molecular targets for immunotherapy. Methods: RNA-seq data and clinical follow-up data of HCC were downloaded from The Cancer Genome Atlas (TCGA) database. Multivariate Cox analysis and Lasso regression were used to identify robust immunity-related genes. Finally, a risk prognosis...

... adenocarcinoma (PDAC). Methods: Based on GSE49149 and the PDAC cohort of The Cancer Genome Atlas (TCGA), differential analyses of promoter methylation, correlation analysis, and Cox regression analysis were performed to identify PMDGs. The promoter methylation level was assessed by bisulfite sequencing...

... trafficking and signal transmission in neuropathy. Participation of YIF1B in serotonin-induced tumor growth and immune regulation has not been previously investigated. Data for analysis of YIF1B mRNA expression were downloaded from the website portals: The Cancer Genome Atlas (TCGA), GTEx, Cancer Cell Line...

.... In our study, the transcriptome expression profile data ( n =89) of chRCC, corresponding clinical data ( n =113) and the somatic mutation data ( n =66) were obtained from the TCGA database. We first analyzed the mutation data of chRCC patients and divided chRCC patients into high and low tumor mutation...

... the role of miR-331-3p in HCC through weighted gene coexpression network analysis (WGCNA) based on The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Oncomine. WGCNA was applied to build gene co-expression networks to examine the correlation between gene sets and clinical characteristics...

..., GSE22866 was downloaded from gene expression omnibus (GEO). The genomic and clinical data were obtained from TCGA. The differentially expressed genes (DEGs) were identified and functional analysis was performed using clusterprofiler. Then, the co-expression network for the DEGs was established using...

... and gene expression profiles of breast cancer patients along with their adjacent normal tissues from the Cancer Genome Atlas (TCGA) were obtained as the training set. CpGs that with significantly elevated methylation level in breast cancer than not only their adjacent normal tissues and the other ten...

... described as a powerful predictor of tumor behavior and response to immunotherapy. Methods: A total of 443 bladder cancer samples obtained from The Cancer Genome Atlas (TCGA) were analyzed for mutation types, TMB values, and prognostic value of TMB. Differentially expressed genes (DEGs) were identified from...

... assessed the relative proportions of 22 TIICs in HNSC using publicly available TCGA transcriptional datasets, analyzed the proportions of TIICs between HNSC tissues and normal tissues, along with accompanying clinicopathological data, and the impact of TIICs on clinical outcome. After the filter criteria...

...Guo Feng; Zhang Beilei; Chen Caizhi; Zou Wen The present study aims to find a differential protein-coding gene caspase 12 ( CASP12 ) in cervical cancer (CC) based on the (TCGA) database and verify its clinical diagnostic and prognostic values. The transcriptome and clinicopathological data of CC...

... year worldwide. The determination of key microRNAs for the prognosis of ESCA is of indispensable significance in the clinical treatment. Methods The differentially expressed microRNAs were screened by analyzing The Cancer Genome Atlas (TCGA) database. By using the survival data of the database, we...

... development and prognosis remains unclear. In the present study, the expression of MALAT1 in clinical samples of breast cancer tissues was found to be significantly up-regulated that was consistent with the result based on the dataset of the Cancer Genome Atlas (TCGA) at cBioportal. A negative correlation...

... the transcriptional regulation of tumour uricogenesis in human tumours, and relate uricogenesis with tumour pathological and pharmacological findings. Using data from The Cancer Genome Atlas (TCGA), we analysed the expression levels of xanthine dehydrogenase (XDH) and adenine phosphoribosyltransferase (APRT), two key...