Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq/Experiment 2
Subjects
- Location of subjects
- China
- 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
- Triple-negative breast cancer triple-negative breast cancer,triple-negative breast carcinoma,triple-receptor negative breast cancer,Triple-negative breast cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal breast tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- triple-negative breast cancer tumor tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- RNA-seq transcriptomic data obtained from triple-negative breast cancer patients in China (Data taken from study PRJNA553096)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 72
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
- 5.5
Signature 1
Source: Figure 3 (B)
Description: Differentially represented taxa between normal breast tissue samples and breast tumour tissue. (B) Comparison of microbiome in primary tumours of 72 patients from China and 18 normal breast tissues of cancer-free donors from China. For visualisation, LEfSe was run with parameters (LDA > 5.5, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05), for the purpose of visualising the best hits.
Abundance in Group 1: increased abundance in triple-negative breast cancer tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Bacillales | ||
| Bacillaceae | ||
| Achromobacter | ||
| Peptostreptococcaceae | ||
| Alcaligenaceae |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 3 (B)
Description: Differentially represented taxa between normal breast tissue samples and breast tumour tissue. (B) Comparison of microbiome in primary tumours of 72 patients from China and 18 normal breast tissues of cancer-free donors from China. For visualisation, LEfSe was run with parameters (LDA > 5.5, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05), for the purpose of visualising the best hits.
Abundance in Group 1: decreased abundance in triple-negative breast cancer tumor tissue
Revision editor(s): Ecsharp
