Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq/Experiment 5
Subjects
- Location of subjects
- Slovakia
- 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
- 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
- HER2- BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HER2+ BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients with HER2 status (HER+ vs HER-). 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity and HER2 status.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Kruskall-Wallis
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 4 (C)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (C) Comparison of the microbiome in primary tumours of patients positive on HER2 marker and negative on HER2 marker status.
Abundance in Group 1: increased abundance in HER2+ BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter pylori | ||
| Musicola paradisiaca | ||
| Pseudactinotalea sp. HY158 | ||
| Paraburkholderia fungorum | ||
| Massilia oculi | ||
| Burkholderiales | ||
| Betaproteobacteria |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4 (C)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (C) Comparison of the microbiome in primary tumours of patients positive on HER2 marker and negative on HER2 marker status.
Abundance in Group 1: decreased abundance in HER2+ BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Flavobacteriia | ||
| Flavobacteriales | ||
| Weeksellaceae | ||
| Nocardioides | ||
| Deinococci | ||
| Deinococcota |
Revision editor(s): Ecsharp
