Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq/Experiment 1
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
- normal breast tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- breast cancer tumor tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients (stage I–III) treated with surgery from April 2012 to February 2015
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
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 3 (A)
Description: Differentially represented taxa between normal breast tissue samples (from cancer-free donors) and breast tumour tissue. (A) Comparison of the microbiome in primary tumours of Slovak patients and normal breast tissue of Slovak cancer-free donors. Since standard conditions identified too many results, to visualise data, LEfSe was run with parameters (LDA > 3, Kruskal Wallis testp-value < 0.05, Wilcoxon testp-value < 0.05)
Abundance in Group 1: increased abundance in breast cancer tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Rhodobacter | ||
| Micrococcus | ||
| Priestia megaterium | ||
| Priestia | ||
| Mycobacteriales | ||
| Acinetobacter | ||
| Caudoviricetes | ||
| Gorganvirus isfahan | ||
| Gorganvirus | ||
| Uroviricota | ||
| Viruses |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 3 (A)
Description: Differentially represented taxa between normal breast tissue samples (from cancer-free donors) and breast tumour tissue. (A) Comparison of the microbiome in primary tumours of Slovak patients and normal breast tissue of Slovak cancer-free donors. Since standard conditions identified too many results, to visualise data, LEfSe was run with parameters (LDA > 3, Kruskal Wallis testp-value < 0.05, Wilcoxon testp-value < 0.05)
Abundance in Group 1: decreased abundance in breast cancer tumor tissue
Revision editor(s): Ecsharp
