Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2021/03/20
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
- 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
- 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
- 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+ persistence
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV infection of the same type that lasts for more than 12 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- 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
- 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
- Ion Torrent
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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 5
Description: LEfSe Analysis. A: LDA value distribution histogram
Abundance in Group 1: increased abundance in HPV+ persistence
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 5
Description: LEfSe Analysis. A: LDA value distribution histogram
Abundance in Group 1: decreased abundance in HPV+ persistence
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus | ||
Lactobacillaceae | ||
Lactobacillales | ||
Bacilli | ||
Bacillota |
Revision editor(s): Cynthia Anderson
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+ transient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV infection cleared within 12 months
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 5
Description: LEfSe Analysis. A: LDA value distribution histogram
Abundance in Group 1: increased abundance in HPV+ transient
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus iners |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 5
Description: LEfSe Analysis. A: LDA value distribution histogram
Abundance in Group 1: decreased abundance in HPV+ transient
NCBI | Quality Control | Links |
---|---|---|
Lactobacillales | ||
Lactobacillaceae | ||
Lactobacillus | ||
Bacilli | ||
Bacillota |
Revision editor(s): Cynthia Anderson