Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T0-T2 low tumor stages patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T3-T4 high tumor stages patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not stated
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Figure 4 +text
Description: Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.
Abundance in Group 1: increased abundance in T3-T4 high tumor stages patients
NCBI | Quality Control | Links |
---|---|---|
Parvimonas |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4 +text
Description: Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.
Abundance in Group 1: decreased abundance in T3-T4 high tumor stages patients
NCBI | Quality Control | Links |
---|---|---|
Actinomyces | ||
Actinomycetota |
Revision editor(s): WikiWorks