Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
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
- Pancreas Pancreas,pancreas
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Pancreatic ductal adenocarcinoma ductal adenocarcinoma of pancreas,ductal adenocarcinoma of the pancreas,malignant neoplasm of duct of Wirsung,pancreas ductal adenocarcinoma,pancreatic duct adenocarcinoma,pancreatic duct cancer,pancreatic ductal adenocarcinoma,pancreatic ductal carcinoma,pancreatic tubular adenocarcinoma,Pancreatic ductal adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Adjacent Tissue (NAT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pancreatic ductal adenocarcinoma (PDAC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Pancreatic ductal adenocarcinoma tumor samples.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 105
- Group 1 sample size Number of subjects in the case (exposed) group
- 103
Lab analysis
- 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
- 2b-RAD
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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 2C and D
Description: Differential taxa at the species and genus level identified by LefSe.
Abundance in Group 1: increased abundance in Pancreatic ductal adenocarcinoma (PDAC)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus | ||
| Staphylococcus aureus |
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 2C and D
Description: Differential taxa at the species and genus level identified by LefSe.
Abundance in Group 1: decreased abundance in Pancreatic ductal adenocarcinoma (PDAC)
Revision editor(s): MyleeeA
