Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing/Experiment 1
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Cynthia Anderson, Claregrieve1, Peace Sandy
Subjects
- Location of subjects
- South Korea
- 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
- normal controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cervical intraepithelial neoplasia cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- women with histology proven CIN2/3
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
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
- 2.5
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: 2021/01/10
Curator: Cynthia Anderson
Revision editor(s): LGeistlinger, Cynthia Anderson, WikiWorks
Source: Figure 1
Description: Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer
Abundance in Group 1: increased abundance in cervical intraepithelial neoplasia cases
| NCBI | Quality Control | Links |
|---|---|---|
| Alkaliphilus | ||
| Pseudothermotoga | ||
| Wolbachia |
Revision editor(s): LGeistlinger, Cynthia Anderson, WikiWorks
Signature 2
Source: Figure 1
Description: Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer
Abundance in Group 1: decreased abundance in cervical intraepithelial neoplasia cases
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudoalteromonas | ||
| Psychrobacter |
Revision editor(s): WikiWorks
