Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
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
- adjacent normal tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancer tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric cancer patients who underwent subtotal gastrectomy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 62
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
- 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
- V4-V5
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: supplementary table S5
Description: Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups
Abundance in Group 1: increased abundance in cancer tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Bacillus | ||
| Bacteroides | ||
| Sphingomonas | ||
| Peptostreptococcus | ||
| Streptococcus | ||
| Fusobacterium | ||
| Prevotella sp. |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
Source: supplementary table S5
Description: Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups
Abundance in Group 1: decreased abundance in cancer tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter | ||
| Lactobacillus |
Revision editor(s): Folakunmi
