Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Taiwan
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- Chronic gastritis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastric Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants diagnosed with early and late stage gastric cancer.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- 4.27
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 2(a)
Description: Comparative analysis of differential abundance between chronic gastritis and gastric cancer at the genus levels using LEfSe.
Abundance in Group 1: increased abundance in Gastric Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus | ||
| Fusobacterium | ||
| Haemophilus | ||
| Oscillibacter | ||
| Parabacteroides | ||
| Phascolarctobacterium | ||
| Sutterella | ||
| Veillonella | ||
| unclassified Sutterellaceae |
Revision editor(s): Shulamite, Aleru Divine
Signature 2
Needs review
Source: Figure 2(a)
Description: Comparative analysis of differential abundance between chronic gastritis and gastric cancer at the genus levels using LEfSe.
Abundance in Group 1: decreased abundance in Gastric Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Collinsella | ||
| Pseudomonas | ||
| Enterococcus | ||
| Adlercreutzia | ||
| Acinetobacter |
Revision editor(s): Shulamite, Aleru Divine
