Comparative analysis of racial differences in breast tumor microbiome/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Chloe on 2022/03/15
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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Neoplasm cell process disease,disease of cellular proliferation,neoplasia,neoplasm,neoplasm (disease),neoplastic disease,neoplastic growth,other neoplasm,tumor,tumor disease,Neoplasm
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BNH with TNBC normal tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BNH with TNBC tumor tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor tissue from black non-hispanic patients with triple negative breast cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.
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).
- relative abundances
- 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
- decreased
Signature 1
Reviewed Marked as Reviewed by Chloe on 2022/03/15
Source: Figure 6a
Description: Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.
Abundance in Group 1: decreased abundance in BNH with TNBC tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| unclassified Bradyrhizobiaceae |
Revision editor(s): Chloe, Itslanapark
