A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-19
Curated date: 2022/09/02
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Atrayees, Victoria
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal adenocarcinoma adenocarcinoma of large bowel,adenocarcinoma of large intestine,adenocarcinoma of the large bowel,adenocarcinoma of the large intestine,colorectal (colon or rectal) adenocarcinoma,colorectal adenocarcinoma,colorectum adenocarcinoma,large bowel adenocarcinoma,large intestine adenocarcinoma,Colorectal adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal cancer patients without TP53 mutation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients with TP53 mutation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- diagnosed of colorectal cancer by colonoscopy and histopathology
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics for one month prior to surgery (fecal sample was taken the night before surgery)
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
- 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
- 4
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-19
Source: Figure 5b
Description: LEfSe was used to compare the microbial variation of the TP53
Abundance in Group 1: increased abundance in colorectal cancer patients with TP53 mutation
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium coprostanoligenes |
Revision editor(s): Mary Bearkland
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-19
Curated date: 2022/09/02
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Merit, Atrayees
Source: Figure 5b
Description: LEfSe was used to compare the microbial variation of the TP53
Abundance in Group 1: decreased abundance in colorectal cancer patients with TP53 mutation
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| unclassified Oscillospiraceae |
Revision editor(s): Mary Bearkland, Merit, Atrayees
