Cross-project comparisons for disease markers

GMrepo currently supports two types of cross-project comparisons for disease markers. See details below.

Cross-project and phenotype comparison for a marker taxon

This purpose of this comparison is to show whether a specific taxon:

• Is unique to a disease, or shared across multiple diseases
• Has the same trend across diseases (e.g., always enriched in disease- or health-associated samples), or shows different trends
• Has the same trend in multiple projects of the same disease, or conflicting trends across projects

Here we use two examples to explain what the above purposes mean.

1. Fusobacterium nucleatum

Fusobacterium nucleatum is a known marker for colorectal cancer (CRC).
In GMrepo, we show that it is also a marker for multiple diseases, including:

• Inflammatory Bowel Diseases
• Crohn Disease
• COVID-19
• Clostridium infections

In addition, it shows consistent trends as a disease-enriched marker:

• Not only across the diseases listed above
• But also across multiple projects within the same disease, such as:
• Crohn Disease
• Colorectal Neoplasms (CRC)

2. Dialister invisus

Dialister invisus is also a marker species for multiple diseases:

However, it shows inconsistent trends between diseases.

Marker taxa of a disease across multiple projects

In GMrepo, a disease may be studied in multiple datasets/projects.
To support comparison across those projects, a dedicated page is available for each phenotype pair (e.g., health vs. liver cirrhosis, or adenoma vs. colorectal cancer), showing both consistent and inconsistent disease-associated microbial markers.

Users can check the Phenotype comparisons page for all available phenotype pairs.

Below is an example.

Colorectal Neoplasms (CRC)

In addition to project details and a data table of identified CRC markers (vs. healthy), a tile view is used to visualize markers stratified by project:

Shown above are microbial markers across ten CRC-related projects.