Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women/Experiment 11
From BugSigDB
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- Ductal carcinoma in situ (DCIS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast cancer (BC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
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
- 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
Source: FIG 3 (C)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and DCIS cohort
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium |
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (C)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and DCIS cohort
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Varibaculum | ||
| 1-681-68 | ||
| Anaerostipes | ||
| Actinomyces | ||
| Peptoniphilus | ||
| Finegoldia | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus | ||
| Odoribacter | ||
| Dialister | ||
| Veillonella | ||
| Coprococcus |
Revision editor(s): Rahila
