Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-11
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
- Urine Urine,urine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease progression measurement Disease progression measurement,disease progression measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower risk of progression (LEP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher risk of progression (HEP)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male bladder cancer patients stratified into the higher risk of progression group (HEP, progression score of EORTC ≥ 7) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- 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
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-11
Source: Supplementary Figure 5B
Description: Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)
Abundance in Group 1: increased abundance in Higher risk of progression (HEP)
Revision editor(s): Ayibatari, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-11
Source: Supplementary Figure 5B
Description: Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)
Abundance in Group 1: decreased abundance in Higher risk of progression (HEP)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Bacillota | ||
| Cyanobacteriota | ||
| Lactobacillales | ||
| uncultured Corynebacterium sp. |
Revision editor(s): Ayibatari, Scholastica
