Analysis of oral microbiome in glaucoma patients using machine learning prediction models/Experiment 2
From BugSigDB
Needs review
Subjects
- Location of subjects
- Republic of Korea
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Buccal mucosa Buccal mucosa,buccal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Open-angle glaucoma glaucoma (primary open-angle),glaucoma simplex,glaucoma, open-angle,open angle glaucoma,open-angle glaucoma,pigmentary glaucoma,wide-angle glaucoma,Open-angle glaucoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- POAG (Primary open-angle glaucoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with primary open-angle glaucoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- edgeR
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.00001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Figure 6b, Supplementary Table S2
Description: Differentially abundant taxa between primary open-angle glaucoma patients and control subjects
Abundance in Group 1: increased abundance in POAG (Primary open-angle glaucoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnospiraceae incertae sedis | ||
| Blautia | ||
| Parabacteroides | ||
| Sulfophobococcus |
Revision editor(s): Anne-mariesharp
Signature 2
Needs review
Source: Figure 6b, Supplementary Table S2
Description: Differentially abundant taxa between primary open-angle glaucoma patients and control subjects
Abundance in Group 1: decreased abundance in POAG (Primary open-angle glaucoma)
Revision editor(s): Anne-mariesharp
