Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women/Experiment 6
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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
- Ductal carcinoma in situ (DCIS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast cancer (BC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 2 (C)
Description: Identification of microbial taxa that differentiate BC and DCIS groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium | ||
| Megamonas |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (B)
Description: Identification of microbial taxa that differentiate BC and DCIS groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Epsilonproteobacteria | ||
| Campylobacterales | ||
| Campylobacteraceae | ||
| Campylobacter |
Revision editor(s): Rahila
