A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer/Experiment 1
Curated date: 2022/08/28
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Fatima, Rimsha, Mary Bearkland, Peace Sandy
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
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients
- 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
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
- 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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figures 4b
Description: Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed from features differentially abundant in CRC and HC fecal samples. The criteria for feature selection were LDA score > 4, p < 0.05, Green and red represent the HC group and CRC group, respectively.
Abundance in Group 1: increased abundance in colorectal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bifidobacterium | ||
| Shigella | ||
| Escherichia |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figures 4b
Description: Fig. 4 Difference of fecal microbiota in CRC patients and HC. b. LDA score computed from features differentially abundant in CRC and HC fecal samples. The criteria for feature selection were LDA score > 4, p < 0.05, Green and red represent the HC group and CRC group, respectively.
Abundance in Group 1: decreased abundance in colorectal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella | ||
| Coprobacillus | ||
| Faecalibacterium | ||
| Romboutsia | ||
| Streptococcus | ||
| Agathobacter |
Revision editor(s): Mary Bearkland, Fatima
