🧿️ Overview

CancerHubs Data Explorer is a shiny app which provides an interactive interface for exploring results from the CancerHubs project, now extended to include 11 tumour types.

The following gene subsets are available for exploration:

  • All Genes: The complete list of genes selected by the CancerHubs framework, scored per tumour, regardless of mutation status or external annotation.
  • PRECOG: Genes annotated by the PRECOG database, reflecting significant prognostic associations.
  • Only Mutated: Genes identified as mutated in the tumour dataset, excluding those in PRECOG set.
  • Only PRECOG: Genes which are significant for PRECOG Z-score that are not found mutated in the dataset.

All genes are ranked using a Network Score, which quantifies how many of their direct interaction partners are mutated within a given tumour type. By integrating protein–protein interaction data from BioGRID with tumour-specific mutation profiles, this score highlights genes that are highly connected to dysfunctional or altered pathways, pointing to their potential as central regulators or therapeutic targets in cancer biology.

🔍 Features

This website allows direct interaction with CancerHubs data through several key tabs:

  • View Dataframe : Explore pre-processed gene tables for each tumour type. Choose between All Genes , PRECOG , Only Mutated , and Only PRECOG subsets. Download filtered data as XLSX or CSV.
  • Gene Ranking : Input a gene symbol to check its rank across cancers based on <strong>Network Score</strong>. Visualise and download the results, including a pan-cancer positioning plot.
  • Common Genes : Identify genes that consistently rank in the top N positions across multiple tumours. View results in a dynamic heatmap and export them.
  • Network Plot (3D) : Visualise a 3D network of the top-scoring genes in a tumour dataset. Interactions are mapped based on known BioGRID interactions. Node colour, shape, and size encode multiple annotations.
  • Gene Network (2D) : Explore direct interactors of any gene of interest. Visualise up to 50 interactors with igraph-style layout and download both the network image and tables.

📖 Citation

If you use CancerHubs in your research, please cite our paper:

Ivan Ferrari, Federica De Grossi, Giancarlo Lai, Stefania Oliveto, Giorgia Deroma, Stefano Biffo, Nicola Manfrini

CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs

Briefings in Bioinformatics, Volume 26, Issue 1, January 2025

https://doi.org/10.1093/bib/bbae635








Not Present
Present





PRECOG (circle)
Non-PRECOG (square)
Mutated (large)
Non-mutated (small)

Input Gene
Network Score > 0
Network Score = 0 or Not Available