Characteristics of Vaginal Microbiome in Women with Pelvic Inflammatory Disease in Korea/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- South Korea
- 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
- Pelvic Inflammatory Disease disease (PID), pelvic inflammatory,inflammatory disease (PID), pelvic,pelvic infection,pelvic inflammatory disease,pelvic inflammatory disease, (PID),PID,PID, pelvic inflammatory disease,Pelvic Inflammatory Disease,pelvic Inflammatory Disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pelvic Inflammatory Disease (PID) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vaginal samples from premenopausal women with Pelvic Inflammatory Disease (PID).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
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
- 2.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Table 4
Description: The Kruskal-Wallis H tests and LEfSe analysis of the associations between normal control women and PID patients.
Abundance in Group 1: increased abundance in Pelvic Inflammatory Disease (PID) group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadaceae | ||
| Yersiniaceae | ||
| Gardnerella | ||
| Pseudomonas | ||
| Parvimonas | ||
| unclassified Enterobacteriaceae | ||
| Megasphaera | ||
| Yersinia |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 4
Description: The Kruskal-Wallis H tests and LEfSe analysis of the associations between normal control women and PID patients.
Abundance in Group 1: decreased abundance in Pelvic Inflammatory Disease (PID) group
Revision editor(s): Aleru Divine
