Tumour-associated and non-tumour-associated microbiota in colorectal cancer/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-2
Subjects
- Location of subjects
- Ireland
- 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
- Intestinal mucosa Bowel mucosa,Bowel mucosa of organ,Bowel mucous membrane,Bowel organ mucosa,Intestine mucosa,Intestine mucosa of organ,Intestine mucous membrane,Intestine organ mucosa,Mucosa of bowel,Mucosa of intestine,Mucosa of organ of bowel,Mucosa of organ of intestine,Mucous membrane of bowel,Mucous membrane of intestine,Organ mucosa of bowel,Organ mucosa of intestine,Tunica mucosa intestini,Intestinal mucosa,intestinal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma cancer of large bowel,cancer of large intestine,cancer of the large bowel,cancer of the large intestine,carcinoma of colorectum,carcinoma of large bowel,carcinoma of large intestine,carcinoma of the large bowel,carcinoma of the large intestine,colorectal (colon or rectal) cancer,colorectal cancer,colorectal carcinoma,colorectum carcinoma,CRC,large bowel cancer,large bowel carcinoma,large intestine cancer,large intestine carcinoma,Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Distal (and rectal) cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Proximal cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with proximal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-2
Source: Supplementary File: Table S8
Description: Differential mucosal microbiota composition of proximal cancer compared to distal cancer
Abundance in Group 1: increased abundance in Proximal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Faecalibacterium | ||
| Veillonella | ||
| unclassified Clostridium | ||
| unclassified Lachnospiraceae | ||
| Lachnospiraceae incertae sedis |
Revision editor(s): ChiomaBlessing, WikiWorks
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-2
Source: Supplementary File: Table S8
Description: Differential mucosal microbiota composition of proximal cancer compared to distal cancer
Abundance in Group 1: decreased abundance in Proximal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Halomonas | ||
| Shewanella |
Revision editor(s): ChiomaBlessing, WikiWorks
