Signatures within the esophageal microbiome are associated with host genetics, age, and disease/Experiment 17
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
Subjects
- Location of subjects
- Australia
- 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
- Esophagus Gullet,Oesophagus,Esophagus,esophagus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GERD(Gastroesophageal reflux disease)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Glandular mucosa (GM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients with Glandular mucosa
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
Source: Additional file 3, sheet 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: increased abundance in Glandular mucosa (GM)
Revision editor(s): Fiddyhamma, Ifeanyisam, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-10
Source: Additional file 3, sheet 5
Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).
Abundance in Group 1: decreased abundance in Glandular mucosa (GM)
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas gingivalis |
Revision editor(s): Fiddyhamma, WikiWorks
