The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-13
Subjects
- Location of subjects
- Austria
- 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
- Squamous cell carcinoma carcinoma, squamous cell, malignant,epidermoid carcinoma,epidermoid cell cancer,malignant epidermoid cell neoplasm,malignant epidermoid cell tumor,malignant squamous cell neoplasm,malignant squamous cell tumor,squamous carcinoma,squamous cell cancer,squamous cell carcinoma,squamous cell carcinoma (morphologic abnormality),squamous cell carcinoma NOS (morphologic abnormality),squamous cell epithelioma,Squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oropharyngeal Squamous Cell Carcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- diagnosed with OSCC and SCC of the oral cavity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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).
- raw counts
- Statistical test
- DESeq2
- 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
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-13
Source: Figure 3, Text
Description: Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls
Abundance in Group 1: increased abundance in Oropharyngeal Squamous Cell Carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bifidobacterium | ||
| Desulfovibrio | ||
| Leptotrichiaceae | ||
| Moryella | ||
| Schwartzia | ||
| Selenomonas | ||
| Treponema |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-13
Source: Figure 3, Text
Description: Significant taxa in patients with oropharyngeal squamous cell carcinoma VS controls
Abundance in Group 1: decreased abundance in Oropharyngeal Squamous Cell Carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Catonella | ||
| Haemophilus | ||
| Neisseria | ||
| Pasteurellaceae | ||
| Prevotella | ||
| Prevotellaceae | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): WikiWorks, ChiomaBlessing
