UALCAN: An update to the integrated cancer data analysis platform

• DOI: 10.1016/j.neo.2022.01.001
• Publication Date: 2022-01-22T22:22:34Z
• Authors: Darshan Shimoga C...; Santhosh Kumar Ka...; Praveen Kumar Korla; Henalben Patel; Ahmedur Rahman Sh...; Mohammad Athar; George J. Netto; Zhaohui S. Qin; Sidharth Kumar; Upender Manne; Chad J. Creighton; Sooryanarayana Va...
• Keywords: Data Analysis; Proteomics; 0301 basic medicine; Original article; UALCAN; Bioinformatics; Gene Expression Profiling; Cancer gene expression; Neoplasms. Tumors. Oncology. Including cancer and carcinogens; Genomics; DNA Methylation; 3. Good health; 03 medical and health sciences; lncRNA; Neoplasms; Patient survival; Humans; Transcriptomics; RC254-282

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.