<div class="title-panel">CancerHubs Data Explorer</div>

Introduction

In this section, you can explore the original datasets used throughout the CancerHubs analysis.

The primary dataset, All Genes, contains all genes identified based on their mutational status and/or relevance in the PRECOG database.

The other three datasets represent filtered subsets:

PRECOG (Mutated or Not) – genes in PRECOG, regardless of mutation
Only MUTATED (Not Precog) – mutated genes not relevant in PRECOG
Only PRECOG (Not Mutated) – PRECOG genes without detected mutations

Each gene is ranked by its Network Score, which reflects its topological importance and potential biological relevance based on its interactions (derived from BioGRID).

You can use this panel to:

Select tumour-specific datasets
Interactively explore gene-level information
Download complete tables for external analysis

Select Cancer Type:

Select Dataframe:

Download Dataframe (XLSX)

Gene Ranking

This panel allows you to investigate the rank of any gene of interest across all tumour types available in the CancerHubs dataset.

Each gene is ranked within each tumour type according to its Network Score, reflecting how central and biologically relevant it is, based on its interactions with other genes in that specific dataset.

You can view:

A plot showing the gene's rank (and its percentile) across selected tumour types
The Pan-Cancer Score, summarising the ranks across all tumours

All plots and tables can be downloaded for further use.

Enter Gene Name:

Select Dataframe Subset:

Download Plot (PDF) Download Ranking Table (XLSX) Download Pan-Cancer Ranking (XLSX)

Common Genes

This panel helps identify genes that are ranked among the most relevant (Top), on the basis of their Network Score, across multiple tumour types.

Genes are selected based on their Network Score, which reflects their importance in tumour-specific interaction networks.

By adjusting the parameters, you can:

Select how many top-ranking genes to consider from each tumour type
Set a threshold for how many tumors a gene must appear in to be included

The output includes:

A downloadable table listing the selected genes and the tumour types in which they recur
An interactive heatmap showing gene presence across tumours (for the image download click on the top-rigth corner of the plot)*

*The number of top genes selected also determines the number of rows in this heatmap.

Number of TOP genes:

Choose Dataframe to View:

Min. Presence in Tumors:

Download Extracted Data (XLSX)

Network Plot

This panel displays an interactive network of the top-ranking genes (based on Network Score) for a selected tumour type.

Each node represents a gene, and edges indicate known interactions among the selected top genes.

By adjusting the parameters, you can:

Choose the number of top genes to visualise
Restrict nodes to mutated interactors only
Switch the coloring of nodes to show their Network Score or their PRECOG metaZ

All network data — including the nodes and their connections — can be downloaded as Excel tables. For image download, use the toolbar in the top-right corner of the network panel.

Select Tumor:

Select Dataset Type:

Color by:

Number of Top Genes:

Include Only Mutated Interactors

Download Edges Table (XLSX)
Download Nodes Table (XLSX)

Gene Network

This panel allows you to explore the interaction partners of a specific gene of interest, selected from the CancerHubs dataset.

The central input genes are selected through the Select Dataset dropdown, and are sourced from the already established CancerHubs categories.
Up to 50 interactors are shown, prioritised — when possible — by Network Score. Interactors without scores are displayed only if no ranked alternatives are available. These interactors are not relevant to CancerHubs nor found in the previously displayed tables.
In the downloadable tables all the interactors are included, whether ranked or not.

The option to include Only Mutated interactors specifically refers to interactors, not to the central input gene.

Depending on the dataset category selected:

In All Genes and Only Mutated, interactors are consistent with the initial raw tables (check 'View Dataframe')
In PRECOG and Only PRECOG, gene's interactors must be PRECOG genes

You can also enable cross-connections among interactors to show shared neighbours.

Select Tumor:

Select Dataset Type:

Enter Gene Name:

Include Only Mutated Interactors

Show all the interactions

Downloads

Here is available the network plot and the complete table of interactions for your interest gene.

Download Network Plot Image (PDF) Download your Gene Interactions (XLSX)

For further analysis is also available the WHOLE dataset of interactions for all the genes that match your paramters selection.

Download WHOLE Interactome Tables (XLSX)

Contact

For questions or support, please contact:

manfrini@ingm.org
ferrari@ingm.org
arsuffi@ingm.org

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

License

Funding

This research was funded by Associazione Italiana per la Ricerca sul Cancro (AIRC), under MFAG 2021 ID 26178 project to Nicola Manfrini.

CancerHubs Data Explorer