16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Victoria
Subjects
- Location of subjects
- United States of America
- 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
- HPV -
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV +
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Text
Description: Relative abundance of oral microbiome in HNSCC HPV + and HPV -
Abundance in Group 1: increased abundance in HPV +
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Weeksella |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
Source: Figure 6, Text
Description: Relative abundance of oral microbiome in HNSCC HPV + and HPV -
Abundance in Group 1: decreased abundance in HPV +
| NCBI | Quality Control | Links |
|---|---|---|
| Eikenella | ||
| Neisseria | ||
| Leptotrichia |
Revision editor(s): WikiWorks
