Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment/Experiment 1
From BugSigDB
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 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
- 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
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
