A comprehensive analysis of breast cancer microbiota and host gene expression/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast carcinoma breast cancer,breast cancer, NOS,breast carcinoma,cancer of breast,cancer of the breast,cancer, breast,carcinoma of breast,carcinoma of the breast,mammary carcinoma,Breast carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with breast cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 668
- Group 1 sample size Number of subjects in the case (exposed) group
- 72
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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).
- raw counts
- Statistical test
- DESeq2
- 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)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/07/28
Source: Figure 3 +text
Description: Species compositions of the Breast Caner and Non-cancerous Adjacent tissues
Abundance in Group 1: increased abundance in Breast Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Alkalihalobacillus alcalophilus | ||
| Brachybacterium muris | ||
| Furfurilactobacillus rossiae | ||
| Salmonella enterica | ||
| Mycolicibacterium phlei | ||
| Mycolicibacterium fortuitum |
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/07/28
Source: Figure 3 +text
Description: Species compositions of the Breast Caner and Non-cancerous Adjacent tissues
Abundance in Group 1: decreased abundance in Breast Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter radioresistens | ||
| Escherichia coli | ||
| Ralstonia pickettii | ||
| Microbacterium barkeri |
