ChromoHub V2: cancer genomics.

Area of Science:

• Genomics
• Epigenetics
• Cancer Biology

Background:

• Epigenetic mechanisms are central to cancer development.
• Chromohub is an existing open-access interface for mapping data onto protein family phylogenies.
• Previous versions focused on chromatin-signaling protein families.

Purpose of the Study:

• To introduce a new cancer genomics interface integrated into Chromohub.
• To enable visualization of cancer-related genomic alterations in epigenetic factors.
• To facilitate exploration of the cancer genomics landscape for chromatin-related proteins.

Main Methods:

• Integrated data from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC).
• Extracted mutation, amplification, and expression change frequencies for chromatin factors.
• Mapped this cancer genomics data onto phylogenetic trees of epigenetic protein families within Chromohub.

Main Results:

• Cancer genomics data for chromatin factors are now accessible through Chromohub.
• Users can visualize the frequency of alterations (mutation, amplification, expression change) in epigenetic proteins across cancer cohorts.
• The interface allows navigation through the cancer genomics landscape of histone modifiers, remodelers, and chaperones.

Conclusions:

• The new Chromohub interface enhances the study of cancer genomics by integrating epigenetic data.
• It provides a powerful tool for researchers to explore the role of chromatin factors in various cancers.
• Facilitates a deeper understanding of epigenetic dysregulation in cancer through interactive data visualization.