Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women/Experiment 8
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Mammographic density measurement Mammographic density measurement,mammographic density measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low breast density
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High breast density
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Comparing high and low breast density.
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 6 (C)
Description: Differentially enriched taxa abundance in fecal samples between high and low breast density was identified using LEfSe analysis (logarithmic LDA score threshold = 3; P < 0.05).
Abundance in Group 1: increased abundance in High breast density
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Phascolarctobacterium | ||
| Cyanobacteriota | ||
| 4C0d-24C0d-2 | ||
| YS2YS2 |
Revision editor(s): Rahila
Signature 2
Source: FIG 6 (C)
Description: Differentially enriched taxa abundance in fecal samples between high and low breast density was identified using LEfSe analysis (logarithmic LDA score threshold = 3; P < 0.05).
Abundance in Group 1: decreased abundance in High breast density
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae |
Revision editor(s): Rahila
