Variations in oral microbiota associated with oral cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Subjects
- Location of subjects
- China
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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
- Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- oral squamous cell carcinoma (OSCC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 1c, Figure 3b, 3c, Text
Description: Variations in oral microbiota associated with oral cancer
Abundance in Group 1: increased abundance in oral squamous cell carcinoma (OSCC)
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 1c, Figure 3b, 3c, Text
Description: Variations in oral microbiota associated with oral cancer
Abundance in Group 1: decreased abundance in oral squamous cell carcinoma (OSCC)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Stomatobaculum | ||
| Granulicatella | ||
| Lautropia | ||
| Veillonella | ||
| Streptococcus | ||
| Scardovia | ||
| Rothia | ||
| Actinomyces | ||
| Actinomycetota | ||
| Bacillota |
Revision editor(s): WikiWorks
