The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- South Africa
- 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
- Uterine cervix Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
- 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
- low risk hpv
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high risk hpv
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High risk HPV infection confirmed through HPV genotyping test
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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)
- 0.2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 4
Description: Potential biomarkers for high-risk HPV by LefSe
Abundance in Group 1: increased abundance in high risk hpv
| NCBI | Quality Control | Links |
|---|---|---|
| Azotobacter group | ||
| Aerococcaceae | ||
| Coriobacteriales | ||
| Coriobacterium | ||
| Actinomycetota | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Fusobacteriales | ||
| Fusobacteriota |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 4
Description: Potential biomarkers for high-risk HPV by LefSe
Abundance in Group 1: decreased abundance in high risk hpv
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurellales | ||
| Pasteurellaceae | ||
| Haemophilus | ||
| Alphaproteobacteria | ||
| Gammaproteobacteria | ||
| Pseudomonadales | ||
| Phyllobacterium | ||
| Hyphomicrobiales | ||
| Phyllobacteriaceae |
Revision editor(s): WikiWorks
