Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-21
Subjects
- Location of subjects
- Egypt
- 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
- Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal samples free from Colorectal Cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Egyptian Samples with Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Egyptian Patients with colocrectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-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 2024-2-20
Source: Figure 2A
Description: Fig.2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in Egyptians.
Abundance in Group 1: increased abundance in Egyptian Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Abyssicoccus albus | ||
| Bifidobacterium pseudolongum | ||
| Corynebacterium kroppenstedtii | ||
| Cutibacterium acnes | ||
| Eubacteriales | ||
| Kocuria | ||
| Lactobacillus helveticus | ||
| Tissierella creatinophila |
Revision editor(s): Chloe 256, Peace Sandy, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-20
Source: Figure 2A
Description: Figure 2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in egyptians.
Abundance in Group 1: decreased abundance in Egyptian Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Exiguobacterium | ||
| Kocuria palustris | ||
| Micrococcus | ||
| Neisseria | ||
| Pseudomonas viridiflava | ||
| Rothia aeria |
Revision editor(s): Chloe 256, Peace Sandy
