Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
- 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 adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma,Gastric adenocarcinoma
- 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
- Gastric cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gastric carcinoma confirmed by pathological examination
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
- 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Supplementary figure 3
Description: Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched
Abundance in Group 1: increased abundance in Gastric cancer
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Supplementary figure 3
Description: Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched
Abundance in Group 1: decreased abundance in Gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderiales | ||
| Betaproteobacteria | ||
| Clostridia | ||
| Eubacteriales | ||
| Lachnospiraceae | ||
| Agathobacter rectalis CAG:36 | ||
| Roseburia | ||
| Lachnospira | ||
| Lachnoclostridium |
Revision editor(s): WikiWorks
