Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- Nigeria
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-/HIV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+/HIV-
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HR-HPV+ confirmed by medical records and HPV genotyping test
- Group 0 sample size Number of subjects in the control (unexposed) group
- 99
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
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
Signature 1
Needs review
Source: Fig. 4b
Description: Identified phylotype biomarkers ranked by effect size in HIV–women
Abundance in Group 1: increased abundance in HPV+/HIV-
Signature 2
Needs review
Source: Fig. 4b
Description: Identified phylotype biomarkers ranked by effect size in HIV–women
Abundance in Group 1: decreased abundance in HPV+/HIV-
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria | ||
| Halorubrum | ||
| Halorubrum sp. | ||
| Hyphomicrobiales | ||
| Lactobacillus iners | ||
| Lysobacterales | ||
| Lactobacillus | ||
| Lactobacillales |
