Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer/Experiment 2
From BugSigDB
Subjects
- Location of subjects
- Botswana
- 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
- Cervix squamous epithelium Cervical squamous epithelium,Cervix squamous epithelium,cervix squamous epithelium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical cancer cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,Cervical cancer,cervical cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV Positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV positive cervical dysplasia and cervical cancer patient’s
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
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
- 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)?
- No
- 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
Signature 1
Source: Figure 1E
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia HIV positive and negative patients using LefSe analysis.
Abundance in Group 1: increased abundance in HIV Positive
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichia | ||
| Erysipelotrichales | ||
| Erysipelotrichaceae | ||
| Ruminiclostridium | ||
| Bacilli | ||
| Lactobacillales |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 1E
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia HIV positive and negative patients using LefSe analysis.
Abundance in Group 1: decreased abundance in HIV Positive
| NCBI | Quality Control | Links |
|---|---|---|
| Filifactor |
Revision editor(s): MyleeeA
