Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women/Experiment 3
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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Genital neoplasm, female cancer of female reproductive organ,female reproductive cancer,female reproductive organ cancer,gynecologic cancer,malignant female reproductive organ neoplasm,malignant female reproductive system neoplasm,malignant female reproductive system tumor,malignant gynecologic neoplasm,malignant gynecologic tumor,malignant neoplasm of female genital organ,malignant neoplasm of female reproductive organ,malignant neoplasm of female reproductive system,malignant neoplasm of the female reproductive system,malignant tumor of female reproductive system,malignant tumor of the female reproductive system,Genital neoplasm, female,genital neoplasm, female
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-RT GynCa groups (Gynecologic cancer patients Pre-radiation therapy).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal women with Gynecologic cancer post-radiation therapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 65
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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).
- relative abundances
- Statistical test
- LEfSe
- 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
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 3b
Description: Differentially abundant bacterial operational taxonomic units between pre- and post-RT (radiation therapy) vaginal microbiomes.
Abundance in Group 1: increased abundance in Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).
Revision editor(s): Tosin
Signature 2
Source: Figure 3b
Description: Differentially abundant bacterial operational taxonomic units between pre- and post-RT vaginal microbiomes.
Abundance in Group 1: decreased abundance in Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).
| NCBI | Quality Control | Links |
|---|---|---|
| Sutterella | ||
| Oscillospiraceae |
Revision editor(s): Tosin
