Breast tissue, oral and urinary microbiomes in breast cancer/Experiment 3
From BugSigDB
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
- Urine Urine,urine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Menopause Change of Life, Female,Menopause,menopause
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peri/postmenopausal women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Urine samples from patients with peri/postmenopausal menopausal status from the entire cohort, consisting of both cancer and healthy patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
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
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table 4: B) Urine
Description: Taxa Significantly Different in Premenopausal vs. Peri/Postmenopausal Patient Samples by Wilcoxon Rank Sum
Abundance in Group 1: increased abundance in Peri/postmenopausal women
Revision editor(s): Ecsharp
Signature 2
Source: Supplementary Table 4: B) Urine
Description: Taxa Significantly Different in Premenopausal vs. Peri/Postmenopausal Patient Samples by Wilcoxon Rank Sum
Abundance in Group 1: decreased abundance in Peri/postmenopausal women
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillaceae | ||
| Shuttleworthella | ||
| Lactobacillales | ||
| Bacilli | ||
| Bacillota |
Revision editor(s): Ecsharp
