Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment/Experiment 1
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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8
Subjects
- Location of subjects
- United States of America
- 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
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- 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
- Patient-Matched Normal Colon Tissue Samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colorectal Tumor Samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of primary tumor tissue samples obtained from patients diagnosed with colorectal cancer. They were collected from the site of tumor microenvironment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V6
- 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
- Mann-Whitney (Wilcoxon)
- 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
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8
Source: Figure 2 and 3A
Description: Differentially abundant taxa between matched normal and colorectal cancer microbiomes.
Abundance in Group 1: increased abundance in Colorectal Tumor Samples
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Providencia |
Revision editor(s): Aananditaa, Peace Sandy, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-4-8
Source: Figure 2 and 3A
Description: Differentially abundant taxa between matched normal and colorectal cancer microbiomes.
Abundance in Group 1: decreased abundance in Colorectal Tumor Samples
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides uniformis | ||
| Faecalibacterium prausnitzii | ||
| Lachnospiraceae | ||
| Rikenellaceae | ||
| Ruminococcaceae bacterium D16 |
Revision editor(s): Aananditaa, WikiWorks
