Mucosal microbiome dysbiosis in gastric carcinogenesis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
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
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer,Gastric cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- intestinal metaplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Helicobacter pylori
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: increased abundance in gastric cancer
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: decreased abundance in gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Vogesella | ||
| Methyloversatilis | ||
| Syntrophobacteraceae | ||
| Candidatus Portiera |
Revision editor(s): WikiWorks
