UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses

Abstract

Genomics data from The Cancer Genome Atlas (TCGA) project has led to the comprehensive molecular characterization of multiple cancer types. The large sample numbers in TCGA offer an excellent opportunity to address questions associated with tumo heterogeneity. Exploration of the data by cancer researchers and clinicians is imperative to unearth novel therapeutic/diagnostic biomarkers. Various computational tools have been developed to aid researchers in carrying out specific TCGA data analyses; however there is need for resources to facilitate the study of gene expression variations and survival associations across tumors. Here, we report UALCAN, an easy to use, interactive web-portal to perform to in-depth analyses of TCGA gene expression data. UALCAN uses TCGA level 3 RNA-seq and clinical data from 31 cancer types. The portal's user-friendly features allow to perform: 1) analyze relative expression of a query gene(s) across tumor and normal samples, as well as in various tumor sub-groups based on individual cancer stages, tumor grade, race, body weight or other clinicopathologic features, 2) estimate the effect of gene expression level and clinicopathologic features on patient survival; and 3) identify the top over- and under-expressed (up and down-regulated) genes in individual cancer types. This resource serves as a platform for in silico validation of target genes and for identifying tumor sub-group specific candidate biomarkers. Thus, UALCAN web-portal could be extremely helpful in accelerating cancer research. UALCAN is publicly available at http://ualcan.path.uab.edu.

STRAP Promotes Stemness of Human Colorectal Cancer via Epigenetic Regulation of the NOTCH Pathway

“…This observation is also consistent with previous studies showing that NOTCH signaling is high in early stages of human CRC (33). To further assess the clinical relevance of STRAP expression, TCGA data of 274 colorectal adenocarcinoma (COAD) patients and 41 controls were downloaded from UALCAN: http://ualcan.path.uab.edu/index.html (34). The mRNA level of STRAP was increased in all stages of colorectal cancer tissues compared to the normal tissues (Fig.…”

MethSurv: A Web Tool to Perform Multivariable Survival Analysis Using DNA Methylation Data

“…Multiple public resources such as Wanderer [9], METHHC [10] and MEXPRESS [11] provide a simple user interface to explore the relationship between methylation and gene expression data originating from TCGA. Additionally, tools to perform survival analysis using gene expression data from TCGA are also available to the research community [12][13][14][15][16][17][18][19][20]. However, there are no tools to facilitate the evaluation of the prognostic properties of CpG methylation data.…”

Mortalin contributes to colorectal cancer by promoting proliferation and epithelial–mesenchymal transition

“…Ualcan (http://ualcan.path.uab.edu) is an online available tool, which uses the Cancer Genome Atlas (TCGA) RNA‐seq and clinical data from various cancer types. In this study, Ualcan was used to compare the expression of mortalin across TCGA cancers and to compare tumor and normal samples …”