Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis/Experiment 1
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
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, Confounders controlled for: "Metastasis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Metastasis
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 2A,B and Table S1
Description: Differential taxa at the species and genus level identified by MaAsLin2 (*q < 0.25).
Abundance in Group 1: increased abundance in Pancreatic ductal adenocarcinoma (PDAC)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Cutibacterium | ||
| Cutibacterium acnes | ||
| Cutibacterium granulosum | ||
| Staphylococcus | ||
| Staphylococcus aureus |
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 2A, B and Table S1
Description: Differential taxa at the species and genus level identified by MaAsLin2 (*q < 0.25).
Abundance in Group 1: decreased abundance in Pancreatic ductal adenocarcinoma (PDAC)
Revision editor(s): MyleeeA
