UALCAN: An update to the integrated cancer data analysis platform

Abstract

Cancer genomic, transcriptomic, and proteomic profiling has generated extensive data that necessitate the development of tools for its analysis and dissemination. We developed UALCAN to provide a portal for easy exploring, analyzing, and visualizing these data, allowing users to integrate the data to better understand the gene, proteins, and pathways perturbed in cancer and make discoveries. UALCAN web portal enables analyzing and delivering cancer transcriptome, proteomics, and patient survival data to the cancer research community. With data obtained from The Cancer Genome Atlas (TCGA) project, UALCAN has enabled users to evaluate protein-coding gene expression and its impact on patient survival across 33 types of cancers. The web portal has been used extensively since its release and received immense popularity, underlined by its usage from cancer researchers in more than 100 countries. The present manuscript highlights the task we have undertaken and updates that we have made to UALCAN since its release in 2017. Extensive user feedback motivated us to expand the resource by including data on a) microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and promoter DNA methylation from TCGA and b) mass spectrometry-based proteomics from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). UALCAN provides easy access to pre-computed, tumor subgroup-based gene/protein expression, promoter DNA methylation status, and Kaplan-Meier survival analyses. It also provides new visualization features to comprehend and integrate observations and aids in generating hypotheses for testing. UALCAN is accessible at http://ualcan.path.uab.edu

Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways

“…RPPA profiling data can classify tumors according to subtype, where RPPA antibody-based features may also lend themselves to relevant immunohistochemistry studies. For all cancer types studied, we have added the proteomic datasets to the user-friendly UALCAN data portal 26 , 48 , facilitating differential analyses by protein, giving the research community ready access to our results.…”

Ferroptosis-Related Gene MT1G as a Novel Biomarker Correlated With Prognosis and Immune Infiltration in Colorectal Cancer

“…Transcriptome data of 647 CRC cases and 51 adjacent tumor samples were collected and analyzed from TCGA database ( McCain, 2006 ). Furthermore, multiple databases are used together to validate the MT1G expression, such as GEPIA2 ( Tang et al, 2019 ), UALCAN ( Chandrashekar et al, 2022 ), and TNMplot ( Bartha and Győrffy, 2021 ).…”

Ubiquitylation of unphosphorylated c-myc by novel E3 ligase SCFFbxl8

“… 30 Kaplan–Meier analysis for UCEC was derived from the TCGA database and generated by the UALCAN web platform. 31 Alterations of Cyclin D3 in UCEC data were derived from TCGA database and generated by the cBio Cancer Genomics Portal platform. 32 …”