The Microbiota of Breast Tissue and Its Association with Breast Cancer/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Canada
- 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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer breast cancer,breast tumor,cancer of breast,malignant breast neoplasm,malignant breast tumor,malignant neoplasm of breast,malignant neoplasm of the breast,malignant tumor of breast,malignant tumor of the breast,mammary cancer,mammary neoplasm,mammary tumor,primary breast cancer,Breast cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Normal adjacent tissue, collected outside the marginal zone (approximately 5 cm away from the tumor), from patients with breast cancer (BC) undergoing lumpectomies or mastectomies.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6
- 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).
- centered log-ratio
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Signature 1
Source: Figure 3
Description: Differences in relative abundances of taxa exist between healthy and cancer patients. Significance was based on the Benjamini-Hochberg corrected P value of the Wilcoxon rank test (significance threshold, P < 0.1).
Abundance in Group 1: increased abundance in BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Staphylococcus | ||
| Enterobacteriaceae | ||
| Comamonadaceae |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 3
Description: Differences in relative abundances of taxa exist between healthy and cancer patients. Significance was based on the Benjamini-Hochberg corrected P value of the Wilcoxon rank test (significance threshold, P < 0.1).
Abundance in Group 1: decreased abundance in BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Lactococcus | ||
| Corynebacterium | ||
| Streptococcus | ||
| Micrococcus |
Revision editor(s): Ecsharp
