Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-10
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
- 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 controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Biopsy-confirmed diagnosis of breast cancer prior to initiating any treatment, including surgery, chemotherapy, or radiation therapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not mentioned
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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-10
Source: Figure 2
Description: Linear discriminant analysis effect size (LEfSe) analysis of fecal microbiome at genus level of the participants in the control and BCa group samples
Abundance in Group 1: increased abundance in Breast cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Hungatella | ||
| Tyzzerella |
Revision editor(s): Andre
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-10
Source: Figure 2
Description: Linear discriminant analysis effect size (LEfSe) analysis of fecal microbiome at genus level of the participants in the control and BCa group samples
Abundance in Group 1: decreased abundance in Breast cancer patients
