UALCAN: An update to the integrated cancer data analysis platform

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 t...

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Vydané v:Neoplasia (New York, N.Y.) Ročník 25; s. 18 - 27
Hlavní autori: Chandrashekar, Darshan Shimoga, Karthikeyan, Santhosh Kumar, Korla, Praveen Kumar, Patel, Henalben, Shovon, Ahmedur Rahman, Athar, Mohammad, Netto, George J., Qin, Zhaohui S., Kumar, Sidharth, Manne, Upender, Creighton, Chad J., Varambally, Sooryanarayana
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Elsevier Inc 01.03.2022
Neoplasia Press
Elsevier
Predmet:
Bioinformatics
Cancer gene expression
Correlation
Differential expression
lncRNA
Original article
Patient survival
Proteomics
Transcriptomics
UALCAN
Correlation
UALCAN
lncRNA
Transcriptomics
Patient survival
Proteomics
Differential expression
Cancer gene expression
Bioinformatics
ISSN:1476-5586, 1522-8002, 1476-5586
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Popis
Shrnutí: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
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SourceType-Scholarly Journals-1
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ISSN:1476-5586
1522-8002
1476-5586
DOI:10.1016/j.neo.2022.01.001