Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients/Experiment 5
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Subjects
- Location of subjects
- Kenya
- 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
- Colorectal mucosa Colorectal mucosa,colorectal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Population Population,population
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Egyptian, African American and European American Patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of kenyans
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor samples of kenyan patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Curated date: 2023/11/14
Curator: Chloe 256
Revision editor(s): Chloe 256, MyleeeA, Folakunmi, Joan Chuks
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in Tumor samples of kenyans
Revision editor(s): Chloe 256, MyleeeA, Folakunmi, Joan Chuks
