Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas/Experiment 1
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, 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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Head and neck squamous cell carcinoma carcinoma of the head and neck,craniocervical region squamous cell carcinoma,head and neck squamous cell carcinoma,HNSCC,SCCHN,squamous cell carcinoma of head and neck,squamous cell carcinoma of the head and neck,squamous cell carcinoma, head and neck,squamous cell carcinomas of head and neck,Head and neck squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal adjacent tissues
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- squamous cell carcinoma tissues
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- tissues with evidence of squamous cell carcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 121
- Group 1 sample size Number of subjects in the case (exposed) group
- 121
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Sanger
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3 +text
Description: Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.
Abundance in Group 1: increased abundance in squamous cell carcinoma tissues
| NCBI | Quality Control | Links |
|---|---|---|
| Tissierellaceae | ||
| Parvimonas |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3 +text
Description: Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.
Abundance in Group 1: decreased abundance in squamous cell carcinoma tissues
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Actinomycetes | ||
| Actinomycetales | ||
| Actinomycetaceae | ||
| Actinomyces |
Revision editor(s): WikiWorks
