The vaginal microbiome is associated with endometrial cancer grade and histology/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
Subjects
- Location of subjects
- United States of America
- 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
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Endometrial cancer cancer of endometrium,endometrial Ca,endometrial cancer,endometrial neoplasm,endometrium cancer,malignant endometrial neoplasm,malignant endometrium neoplasm,malignant neoplasm of endometrium,neoplasm of endometrium,primary malignant neoplasm of endometrium,tumor of endometrium,Endometrial cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Benign
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Grade
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low Grade refers to patients with low grade endometrial cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 14 days
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- BGISEQ-500 Sequencing
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
Source: Fig. 3D
Description: Differential abundance of taxa between Low grade and Benign patients
Abundance in Group 1: increased abundance in Low Grade
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. | ||
| Corynebacterium amycolatum | ||
| Lactobacillus gasseri | ||
| Peptoniphilus duerdenii | ||
| Porphyromonas uenonis |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
Source: Fig. 3D
Description: Differential abundance of taxa between Low grade and Benign patients
Abundance in Group 1: decreased abundance in Low Grade
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus epidermidis |
Revision editor(s): KateRasheed
