Microbial dysbiosis is associated with human breast cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-26
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
- normal tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- tumor tissue
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
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).
- raw counts
- Statistical test
- T-Test
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-26
Source: Table S2 and Figure 1d
Description: OTUs enriched in paired normal or tumor tissue
Abundance in Group 1: increased abundance in tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Methylobacterium radiotolerans | ||
| Flavobacterium | ||
| Methylobacterium | ||
| Methylobacteriaceae |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-26
Source: Table S2 and Figure 1d
Description: OTUs enriched in paired normal or tumor tissue
Abundance in Group 1: decreased abundance in tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingobium yanoikuyae | ||
| Sphingomonas | ||
| Nitrosomonas | ||
| Novosphingobium aromaticivorans | ||
| Bradyrhizobium | ||
| Streptococcus pseudopneumoniae | ||
| Sphingomonadaceae |
