Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Subjects
- Location of subjects
- China
- India
- Saudi Arabia
- Sri Lanka
- Yemen
- 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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity,Oral squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NAT (Normal Adjacent Tissue)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FEP (Fibroepithelial polyp)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to a benign oral mucosal lesion characterized by fibrous connective tissue overgrowth.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
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).
- arcsine square-root
- Statistical test
- MaAsLin2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- geographic area
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Fig. 4E
Description: Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.
Abundance in Group 1: increased abundance in FEP (Fibroepithelial polyp)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-1
Source: Fig. 4E
Description: Relative abundance of significantly different bacterial genera between pairwise comparisons of the phenotypes in Bios samples.
Abundance in Group 1: decreased abundance in FEP (Fibroepithelial polyp)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Gemella | ||
| Geodermatophilaceae | ||
| Johnsonella | ||
| Oribacterium | ||
| Phascolarctobacterium | ||
| Pseudomonadaceae | ||
| Staphylococcus |
