Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Curated date: 2021/03/19
Curator: Cynthia Anderson
Revision editor(s): WikiWorks, Cynthia Anderson, Claregrieve1, Victoria
Subjects
- Location of subjects
- China
- 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 Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ confirmed by Hybrid Capture II assay
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Source: Figure 2E
Description: Bacterial taxa analysis of the HPV-positive and HPV-negative groups.
Abundance in Group 1: increased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Mycoplasma |
Revision editor(s): Cynthia Anderson
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Curated date: 2021/03/19
Curator: Cynthia Anderson
Revision editor(s): Cynthia Anderson, Claregrieve1
Source: Figure 2E
Description: Bacterial taxa analysis of the HPV-positive and HPV-negative groups.
Abundance in Group 1: decreased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Sporolactobacillaceae | ||
| Sporolactobacillus |
Revision editor(s): Cynthia Anderson, Claregrieve1
