Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population
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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
Subjects
- Location of subjects
- United States of America
- 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
- Cervical glandular intraepithelial neoplasia , Human papilloma virus infection Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia,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
- Atypical Squamous Cells of Undetermined Significance
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Grade Squamous Intraepithelial Lesion
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low grade squamous intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- -V2
- 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
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 58 introitus samples)
Abundance in Group 1: decreased abundance in Low Grade Squamous Intraepithelial Lesion
NCBI | Quality Control | Links |
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Saccharomyces | ||
Sporidiobolaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 2
Subjects
- 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
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8
Description: Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples)
Abundance in Group 1: increased abundance in High risk-HPV
NCBI | Quality Control | Links |
---|---|---|
Malassezia |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Source: Figure 8
Description: Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples)
Abundance in Group 1: decreased abundance in High risk-HPV
NCBI | Quality Control | Links |
---|---|---|
Sporidiobolaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 3
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Atypical Squamous Cells of Undetermined Significance
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Grade Squamous Intraepithelial Lesion
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low grade squamus intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 55 cervical samples)
Abundance in Group 1: decreased abundance in Low Grade Squamous Intraepithelial Lesion
NCBI | Quality Control | Links |
---|---|---|
Sporidiobolaceae |
Revision editor(s): ChiomaBlessing, WikiWorks
Experiment 4
Subjects
- 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
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples)
Abundance in Group 1: increased abundance in High risk-HPV
NCBI | Quality Control | Links |
---|---|---|
Malassezia |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples)
Abundance in Group 1: decreased abundance in High risk-HPV
NCBI | Quality Control | Links |
---|---|---|
Sporidiobolaceae |
Revision editor(s): WikiWorks, ChiomaBlessing