Identification of disease markers in curated projects¶
Please note this is an
ongoing effort and the results are available for a limited number of projects; more projects will be added as the analyses go.
Marker identification was performed for
selected projects referred as
curated projects in
. These projects were selected based on the following criteria (of course in addition to availability of manpower and time):
- high-quality meta-data with clearly defined diseases and healthy controls,
- high-quality of data, and
- enough numbers of both cases and controls, usually more than 20 per group.
marker taxon refers to a genus or species that showed significantly differential abundances between two different groups (e.g., cases vs. controls or different disease stages such as adenoma vs. CRC) using
LEfSe (Linear discriminant analysis effect size)
PMID: 21702898 .
Marker taxa were identified on a per-project basis.
Please consult the "All marker taxa" page for more information.
In GMrepo , manually curation was performed for selected projects in order to:
- select usable runs with clearly defined phenotype,
- merge multiple runs if they correspond to the same sample, and calcualte taxon abundances on per-sample basis instead of per-run basis,
- group samples according to their corresponding phenotypes, and
- identify marker taxa between a pair of phenotypes of intersts, e.g. CRC vs. Health.
Curated projects are highlighted with a symbol. In addition to the project meta data and run table, the project page for curated projects also contains a list of samples manually curated, their phenotypes and corresponding runs. Followed by marker taxa identified from pairs of phenotypes (refers to as phenotype comparisons in our database). Marker taxa are shown in both table view and boxplot view. If a curated project contains more than two phenotype groups, for example,
- Healthy controls,
- Adenoma and
- colorectal cancer (CRC)
multiple phenotype comparisons can be performed, such as
- Healthy control vs. CRC,
- Healthy control vs. Adenoma, and
- Adenoma vs. CRC
in order to identify marker taxa for different disease stages.
See PRJEB6070 for an example.
So far, GMrepo includes: