The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing/Experiment 1
Curated date: 2021/03/21
Curator: Cynthia Anderson
Revision editor(s): Cynthia Anderson, WikiWorks, Peace Sandy
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
- Vaginal fluid Vaginal discharge,Vaginal secretion,Vaginal fluid,vaginal fluid
- 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
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV-16+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HPV-16 positive without lesion confirmed by HPV genotyping assay
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age
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
Curated date: 2021/03/21
Curator: Cynthia Anderson
Revision editor(s): Cynthia Anderson, Peace Sandy
Source: Figure 3(B)
Description: Vaginal microbiome as HPV16-infection markers. (B) Histogram of the LDA scores computed for species differentially abundant between HPV16-positive women and controls. The LDA scores (log10) > 2 are listed
Abundance in Group 1: increased abundance in HPV-16+
Revision editor(s): Cynthia Anderson, Peace Sandy
Signature 2
Source: Figure 3 (B)
Description: Vaginal microbiome as HPV16-infection markers. (B) Histogram of the LDA scores computed for species differentially abundant between HPV16-positive women and controls. The LDA scores (log10) > 2 are listed
Abundance in Group 1: decreased abundance in HPV-16+
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus sp. 1140_ESPC | ||
| Alphapapillomavirus | ||
| Mitosporidium daphniae | ||
| Nakaseomyces glabratus | ||
| Mucor ambiguus | ||
| Nosema bombycis |
Revision editor(s): Peace Sandy
