Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
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
- 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
- Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- <=38.8% 8-OHdG-positive cervical cells
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- >38.8% 8-OHdG-positive cervical cells
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with >38.8% of 8-OHdG-positive cervical cells
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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Supplemental Figure 2
Description: Differentially abundant taxa in >38.8% 8-OHdG-positive cervical cells group VS <=38.8% 8-OHdG-positive cervical cells group
Abundance in Group 1: increased abundance in >38.8% 8-OHdG-positive cervical cells
| NCBI | Quality Control | Links |
|---|---|---|
| Agrobacterium | ||
| Azotobacter group | ||
| Betaproteobacteria | ||
| Burkholderiales | ||
| Comamonadaceae | ||
| Hyphomicrobiales | ||
| Limnohabitans | ||
| Oxalobacteraceae | ||
| Phenylobacterium | ||
| Pseudomonas | ||
| Rhizobiaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Supplemental Figure 2
Description: Differentially abundant taxa in >38.8% 8-OHdG-positive cervical cells group VS <=38.8% 8-OHdG-positive cervical cells group
Abundance in Group 1: decreased abundance in >38.8% 8-OHdG-positive cervical cells
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
