Comparative analysis of racial differences in breast tumor microbiome/Experiment 5
Curated date: 2021/07/26
Curator: Itslanapark
Revision editor(s): WikiWorks, LGeistlinger, Chloe, Itslanapark, Victoria
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
- Ethnic group Ethnicity,race,Ethnic group,ethnic group
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- WNH
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BNH
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Normal tissue from black non-hispanic patients with breast cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 8
Description: Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.
Abundance in Group 1: increased abundance in BNH
| NCBI | Quality Control | Links |
|---|---|---|
| Planococcaceae |
Revision editor(s): Itslanapark
Signature 2
Source: Figure 8
Description: Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.
Abundance in Group 1: decreased abundance in BNH
| NCBI | Quality Control | Links |
|---|---|---|
| Phenylobacterium |
Revision editor(s): Itslanapark
