Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China/Experiment 2
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Rimsha, ChiomaBlessing, Joan Chuks
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
- SalivaSaliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal carcinoma cancer of esophagus,cancer of oesophagus,cancer of the esophagus,carcinoma of esophagus,carcinoma of oesophagus,carcinoma of the esophagus,esophageal cancer,esophageal cancer, NOS,esophageal carcinoma,esophagus carcinoma,Esophageal 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
- Esophageal Squamous cell carcinoma (ESCC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who were suspected to have esophageal cancer under endoscopy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 87
- 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
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Metastats
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol drinking, family history of cancer, education level, sex, smoking status, oral hygiene, diet
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Table 3
Description: Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group
Abundance in Group 1: increased abundance in Esophageal Squamous cell carcinoma (ESCC)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Capnocytophaga | ||
| Elizabethkingia | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus | ||
| Butyrivibrio |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Curated date: 2021/01/10
Curator: Utsav Patel
Revision editor(s): WikiWorks, ChiomaBlessing, KateRasheed
Source: Table 3
Description: Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group
Abundance in Group 1: decreased abundance in Esophageal Squamous cell carcinoma (ESCC)
Revision editor(s): WikiWorks, ChiomaBlessing, KateRasheed
