Microbiota disbiosis is associated with colorectal cancer/Experiment 1
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Curated date: 2023/07/25
Curator: Andre
Revision editor(s): WikiWorks, Deacme, Andre, ChiomaBlessing
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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colorectal Cancer Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- 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
- 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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
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
- unchanged
Signature 1
Curated date: 2023/07/25
Curator: Andre
Revision editor(s): WikiWorks, Deacme, Andre, ChiomaBlessing
Source: Figure 2B, Figure 3
Description: Different structures of gut microbiota between healthy individuals and CRC patients
Abundance in Group 1: increased abundance in Colorectal Cancer Patients
Revision editor(s): WikiWorks, Deacme, Andre, ChiomaBlessing
Signature 2
Curated date: 2023/07/25
Curator: Andre
Revision editor(s): WikiWorks, Deacme, Andre, ChiomaBlessing
Source: Figure 2, Figure 3
Description: Different structures of gut microbiota between healthy individuals and CRC patients
Abundance in Group 1: decreased abundance in Colorectal Cancer Patients
Revision editor(s): WikiWorks, Deacme, Andre, ChiomaBlessing
