Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma/Experiment 2
From BugSigDB
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
- Mucosa of body of stomach Body of stomach mucosa,Body of stomach mucosa of organ,Body of stomach mucous membrane,Body of stomach organ mucosa,Corpus gastricum (ventriculare) mucosa,Corpus gastricum (ventriculare) mucosa of organ,Corpus gastricum (ventriculare) mucous membrane,Corpus gastricum (ventriculare) organ mucosa,Gastric body mucosa,Gastric body mucosa of organ,Gastric body mucous membrane,Gastric body organ mucosa,Mucosa of corpus gastricum (ventriculare),Mucosa of gastric body,Mucosa of organ of body of stomach,Mucosa of organ of corpus gastricum (ventriculare),Mucosa of organ of gastric body,Mucosa of organ of stomach body,Mucosa of stomach body,Mucous membrane of body of stomach,Mucous membrane of corpus gastricum (ventriculare),Mucous membrane of gastric body,Mucous membrane of stomach body,Organ mucosa of body of stomach,Organ mucosa of corpus gastricum (ventriculare),Organ mucosa of gastric body,Organ mucosa of stomach body,Stomach body mucosa,Stomach body mucosa of organ,Stomach body mucous membrane,Stomach body organ mucosa,Mucosa of body of stomach,mucosa of body of stomach
- 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
- NC_gastric
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EIESC_gastric
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gastric biopsy samples were obtained from patients diagnosed with early-stage intramucosal esophageal squamous carcinoma (EIESC).
- 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
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who have used antibiotics 4 weeks before admission.
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
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
