Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
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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
Subjects
- Location of subjects
- Taiwan
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth
- 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
- 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
- Stage 4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- OSCC confirmed by biopsy and pathological findings
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 90
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- relative abundances
- 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
Source: Figure 5, Text
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
Abundance in Group 1: increased abundance in Stage 4
Signature 2
Source: Figure 5, Text
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
Abundance in Group 1: decreased abundance in Stage 4
NCBI | Quality Control | Links |
---|---|---|
Hoylesella nanceiensis | ||
Pseudoleptotrichia goodfellowii | ||
Schaalia georgiae | ||
Actinomyces gerencseriae | ||
Prevotella melaninogenica | ||
Granulicatella adiacens |
Experiment 2
Subjects
- Location of subjects
- China
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage 1
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
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
Source: Figure 1, Supplementary Figure 5A , Text
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
Abundance in Group 1: increased abundance in Stage 1
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1, Supplementary Figure 5A , Text
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
Abundance in Group 1: decreased abundance in Stage 1
NCBI | Quality Control | Links |
---|---|---|
Prevotella melaninogenica | ||
Schaalia odontolytica | ||
Veillonella parvula | ||
Porphyromonas pasteri | ||
Haemophilus parainfluenzae | ||
Rothia mucilaginosa | ||
Streptococcus mitis |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage 2 & 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
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
Source: Figure 1, Supplementary Figure 5B, Text
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
Abundance in Group 1: increased abundance in Stage 2 & 3
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1, Supplementary Figure 5B , Text
Description: Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
Abundance in Group 1: decreased abundance in Stage 2 & 3
NCBI | Quality Control | Links |
---|---|---|
Prevotella melaninogenica | ||
Schaalia odontolytica | ||
Veillonella parvula | ||
Porphyromonas pasteri | ||
Haemophilus parainfluenzae | ||
Streptococcus mitis |
Revision editor(s): WikiWorks