Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Subjects
- Location of subjects
- China
- 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
- Esophageal squamous cell carcinoma ESCC,esophageal epidermoid carcinoma,esophageal scc,esophageal squamous cell cancer,esophageal squamous cell carcinoma,esophagus scc,esophagus squamous cell carcinoma,scc of esophagus,scc of the esophagus,squamous cell car. - esophagus,squamous cell carcinoma of esophagus,squamous cell carcinoma of the esophagus,Esophageal 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
- Oesophageal cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- 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
- 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
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 6
Description: Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC)
Abundance in Group 1: increased abundance in Oesophageal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Actinomycetaceae | ||
| Atopobiaceae | ||
| Atopobium | ||
| Coriobacteriales | ||
| Coriobacteriia |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-26
Source: Figure 6
Description: Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC)
Abundance in Group 1: decreased abundance in Oesophageal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Porphyromonadaceae | ||
| Porphyromonas |
