Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-12-16
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
- Uterine cervixUterine cervix
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical carcinoma cancer of cervix,cancer of the cervix,cancer of the uterine cervix,cancer of uterine cervix,carcinoma cervix uteri,carcinoma of cervix,carcinoma of cervix uteri,carcinoma of the cervix,carcinoma of the cervix uteri,carcinoma of the uterine cervix,carcinoma of uterine cervix,cervical cancer,cervical cancer, NOS,cervical carcinoma,cervix cancer,cervix carcinoma,cervix uteri carcinoma,uterine cervix cancer,uterine cervix carcinoma,Cervical carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cervical Dysplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cervical Cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with moderate or poorly differentiated squamous cell cancer of the cervix.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
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
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-16
Source: Figure 2G
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia patients using LefSe analysis.
Abundance in Group 1: increased abundance in Cervical Cancer patients
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-16
Source: Figure 2G
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia patients using LefSe analysis.
Abundance in Group 1: decreased abundance in Cervical Cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Bacillota | ||
| Lachnospira |
