We have collected genomic data of HNSCC patients from The Cancer Genome Atlas (TCGA)and analyzed them to get deeper insights into the gene expression pattern. Initially, 793 differentially expressed genes (DEGs) were categorized, and their enrichment analysis was performed. Later, a protein鈥損rote...
For RNA-sequencingdifferential gene expressionanalysis, data from the TCGA-COAD and TCGA-READ dataset forprimary tumor, obtained using the Illumina HiSeq platform, were used (downloaded from Genomic Data Commons). Secondary COAD RNA-sequencing dataset from CPTAC-2 was analyzed similarly.4Differential ...
Next, we evaluated whether our model of healthy gene expression could find meaningful representations for cancer samples. To do so, we used our model (trained on GTEx) to find representations for tumor samples (Additional File3: Table S2) from The Cancer Genome Atlas dataset (TCGA). These rep...
The altered expression of PPARG, PTGS2, and PTPRC in mtKRAS and wtKRAS cells was confirmed by using qPCR and in-silico verification using Gene Expression Atlas and TCGA databases. Some limitations of this study should be considered for the better interpretation of the results. The results were...
To analyze the roles of identified ovarian cancer gene biomarkers on patient survival, we used the UALCAN (Chandrashekar et al., 2017) tool to generate Kaplan-Meier (KM) survival plots. The UALCAN tool is based on genomics data from The Cancer Genome Atlas (TCGA). The TCGA (Tomczak et ...
TCGA data portal first went through a log(x + 1) transform, then was quantile-normalized, and finally was corrected for age, batch, race, and gender using a linear regression approach. For the differential correlation analysis of p53/PTEN, this RNA expression data was filtered to contain...
CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. Nucleic Acids Res. 2016;44(7), e62. Article PubMed PubMed Central CAS Google Scholar Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X...
We sub-grouped the study subjects into Caucasians (n = 85) and Asians (n = 114) groups according to the TCGA clinical data (Additional file 1: Table S3) and performed the t-test for group comparison of PSI value to identify differential AS genes between the groups. The numbers...
Surprisingly, we found that only 17–33% of the genes met expected gene expression results based on their methylation status (Figs. 2C and 4D,E). Of note, even in TCGA HGSOC only 168 out of 14,475 probed genes were downregulated in conjunction with DNA hypermethylation15. Given these ...
Different superscripts within a column for each gene denote values that are significantly different from each other. 1 Poly (I:C) = treatment with polyionosinic-polycytidylic acid. Table 2. Differential expression of mRNA (40−ΔCt) of Toll-like receptor (TLR) and interleukin (IL) genes in...