Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-29
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
- Lower part of vagina Caudal vagina,Lower third of vagina,Lower vagina,Perineal part of vagina,Sinus vagina,Vagina lower part,Vaginal bulb,Lower part of vagina,lower part of vagina
- 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
- Endometrial cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients undergoing hysterectomy for endometrial cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 67
- Group 1 sample size Number of subjects in the case (exposed) group
- 57
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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).
- relative abundances
- Statistical test
- Wald Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, menopause, vaginal pH
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 ChiomaBlessing on 2024-2-29
Source: Figure 4 + Table S2
Description: Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients
Abundance in Group 1: decreased abundance in Endometrial cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-29
Source: Figure 4 + Table S2
Description: Bacterial OTUs differentially enriched among patients with endometrial cancer compared to Benign patients
Abundance in Group 1: increased abundance in Endometrial cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Arcanobacterium | ||
| Campylobacter | ||
| Finegoldia | ||
| Fusobacterium | ||
| Gallicola | ||
| Lactobacillus | ||
| Peptococcus | ||
| Peptoniphilus | ||
| Porphyromonas | ||
| Prevotella | ||
| Varibaculum | ||
| Anaerococcus |
Revision editor(s): WikiWorks, ChiomaBlessing
