UALCAN: An update to the integrated cancer data analysis platform

UALCAN: An update to the integrated cancer data analysis platform

2022 | Darshan Shimoga Chandrashekar, Santhosh Kumar Karthikeyan, Praveen Kumar Korla, Henalben Patel, Ahmedur Rahman Shovon, Mohammad Athar, George J. Netto, ZhaoHui S. Qin, Sidharth Kumar, Upender Manne, Chad J. Creighton, Sooryanarayana Varambally
UALCAN is an updated integrated cancer data analysis platform that provides a web portal for exploring, analyzing, and visualizing cancer genomic, transcriptomic, and proteomic data. It enables users to integrate data to better understand gene, protein, and pathway changes in cancer and make discoveries. The platform allows analysis and delivery of cancer transcriptome, proteomics, and patient survival data to the cancer research community. Using data from The Cancer Genome Atlas (TCGA), UALCAN enables users to evaluate protein-coding gene expression and its impact on patient survival across 33 cancer types. Since its release in 2017, the portal has been widely used, with over 750,000 accesses from more than 100 countries. The current manuscript highlights the updates and additions made to UALCAN since its release. User feedback led to the inclusion of data on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and promoter DNA methylation from TCGA, as well as 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 offers new visualization features to help users understand and integrate observations, aiding in hypothesis generation. The platform includes data on non-coding gene expression, DNA methylation, proteomics, and ChIP-seq data. It allows users to analyze gene expression, promoter methylation, and survival data, as well as perform gene correlation analyses and pan-cancer views. UALCAN also includes features for analyzing microRNA and lncRNA expression and survival, as well as promoter DNA methylation. The platform is accessible at http://ualcan.path.uab.edu. UALCAN is a valuable resource for cancer researchers, providing a comprehensive platform for analyzing and interpreting cancer data.UALCAN is an updated integrated cancer data analysis platform that provides a web portal for exploring, analyzing, and visualizing cancer genomic, transcriptomic, and proteomic data. It enables users to integrate data to better understand gene, protein, and pathway changes in cancer and make discoveries. The platform allows analysis and delivery of cancer transcriptome, proteomics, and patient survival data to the cancer research community. Using data from The Cancer Genome Atlas (TCGA), UALCAN enables users to evaluate protein-coding gene expression and its impact on patient survival across 33 cancer types. Since its release in 2017, the portal has been widely used, with over 750,000 accesses from more than 100 countries. The current manuscript highlights the updates and additions made to UALCAN since its release. User feedback led to the inclusion of data on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and promoter DNA methylation from TCGA, as well as 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 offers new visualization features to help users understand and integrate observations, aiding in hypothesis generation. The platform includes data on non-coding gene expression, DNA methylation, proteomics, and ChIP-seq data. It allows users to analyze gene expression, promoter methylation, and survival data, as well as perform gene correlation analyses and pan-cancer views. UALCAN also includes features for analyzing microRNA and lncRNA expression and survival, as well as promoter DNA methylation. The platform is accessible at http://ualcan.path.uab.edu. UALCAN is a valuable resource for cancer researchers, providing a comprehensive platform for analyzing and interpreting cancer data.
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