Microbiota disbiosis is associated with colorectal cancer/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
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
- Colorectal mucosa Colorectal mucosa,colorectal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sigmoid neoplasm neoplasm of sigmoid colon,sigmoid colon neoplasm,sigmoid colon neoplasm (disease),sigmoid colon tumor,sigmoid neoplasm,tumor of sigmoid colon,Sigmoid neoplasm
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Proximal Colon Cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Distal Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)
- 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
- 16
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Fisher's Exact Test
- Chi-Square
- T-Test
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: FIGURE 4
Description: Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level)
Abundance in Group 1: increased abundance in Distal Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Fusobacterium | ||
| Leptotrichia |
Revision editor(s): Andre, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: FIGURE 4
Description: Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level)
Abundance in Group 1: decreased abundance in Distal Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcus | ||
| Prevotella | ||
| Pyramidobacter sp. | ||
| Selenomonas |
Revision editor(s): Andre, ChiomaBlessing
