Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-6
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
- 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 cancer Aerodigestive tract cancer, susceptibility to,Ca lower third oesophagus,Ca middle third oesophagus,cancer of esophagus,Escc, susceptibility to,esophageal cancer,esophageal squamous cell carcinoma, susceptibility to,esophagus cancer,gastric cardia adenocarcinoma, susceptibility to,malignant esophageal neoplasm,malignant esophageal tumor,malignant esophagus neoplasm,malignant esophagus tumor,malignant neoplasm of distal third of esophagus,malignant neoplasm of esophagus,malignant neoplasm of lower third of oesophagus,malignant neoplasm of middle third of oesophagus,malignant neoplasm of proximal third of esophagus,malignant neoplasm of the esophagus,malignant neoplasm of upper third esophagus,malignant tumor of abdominal esophagus,malignant tumor of distal third of esophagus,malignant tumor of esophagus,malignant tumor of proximal third of esophagus,malignant tumor of the esophagus,malignant tumor of the middle third of the esophagus,Esophageal cancer
- 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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-6
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-6
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
