PANDA: PAN Cancer Data Analysis Web Tool

G Pepe; C Notturno Granieri; R Appierdo; G Ausiello; M Helmer-Citterich; P F Gherardini

doi:10.1016/j.jmb.2025.169158

PANDA: PAN Cancer Data Analysis Web Tool

J Mol Biol. 2025 Aug 1;437(15):169158. doi: 10.1016/j.jmb.2025.169158. Epub 2025 Apr 16.

Authors

G Pepe¹, C Notturno Granieri², R Appierdo³, G Ausiello², M Helmer-Citterich⁴, P F Gherardini⁵

Affiliations

¹ Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy. Electronic address: gerardo.pepe@uniroma2.it.
² Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy.
³ Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy; PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
⁴ Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy. Electronic address: manuela.helmer.citterich@uniroma2.it.
⁵ Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy. Electronic address: pier.federico.gherardini@uniroma2.it.

PMID: 40250704
DOI: 10.1016/j.jmb.2025.169158

Abstract

Cancer research faces challenges due to the genetic diversity within tumors and individual variability. Precision medicine aims to identify genomic and molecular factors linked to clinical outcomes, leveraging large datasets for drug discovery and patient stratification. We introduce PANDA (PAN-cancer Data Analysis web tool) (https://panda.bio.uniroma2.it), a web server designed for analyzing TCGA genomic data. A total of 32 tumor types and 10,711 samples were selected for this analysis. PANDA simplifies complex tasks such as differential expression, survival analysis, and patient stratification, incorporating clinical factors like sex, stage, and treatment history. It also enables the exploration of biological pathways and immune cell type proportion, providing insights into tumor progression. PANDA is user-friendly, designed for researchers with limited informatics expertise, and supports diverse analyses to advance cancer research.

Keywords: TCGA patient stratification; cancer biology; cancer genomics; immune cell deconvolution; pan-cancer analysis.

MeSH terms

Computational Biology* / methods
Databases, Genetic
Genomics / methods
Humans
Internet
Neoplasms* / genetics
Precision Medicine / methods
Software*