Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer/Experiment 2
From BugSigDB
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colitis , Cancer Colitides,colitis,colitis (disease),colon inflammation,inflammation of colon,Colitis,CA,cancer,cell type cancer,malignancy,malignant Growth,malignant neoplasm,malignant neoplasm (disease),malignant neoplastic disease,malignant tumor,MT,neoplasm (disease), malignant,neoplasm, malignant,organ system cancer,primary cancer,Cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice with inflammation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice with dysplasia/cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM and 1–2 DSS cycles
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- Statistical test
- edgeR
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S3
Description: OTUs distinguishing inflammation from colorectal cancer, highlighting taxa involved in cancer-related microbiome changes.
Abundance in Group 1: increased abundance in Mice with dysplasia/cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Prevotella |
Revision editor(s): Wendy640
Signature 2
Source: Table S3
Description: OTUs distinguishing inflammation from colorectal cancer, highlighting taxa involved in cancer-related microbiome changes.
Abundance in Group 1: decreased abundance in Mice with dysplasia/cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae |
Revision editor(s): Wendy640
