Potential of fecal microbiota for early-stage detection of colorectal cancer
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2022/01/10
Curator: Itslanapark
Revision editor(s): Itslanapark, Fatima, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- France
- 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 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
- Neoplasia-free
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients referred for colonoscopy that had cancerous tumors
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)
- .1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa
Abundance in Group 1: increased abundance in CRC patients
Revision editor(s): Itslanapark, Fatima
Signature 2
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa
Abundance in Group 1: decreased abundance in CRC patients
Revision editor(s): Itslanapark, Fatima
Experiment 2
Subjects
- 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
- Adenoma patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa between CRC and Adenoma patients
Abundance in Group 1: increased abundance in CRC patients
Revision editor(s): Fatima
Signature 2
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa between CRC and Adenoma patients
Abundance in Group 1: decreased abundance in CRC patients
NCBI | Quality Control | Links |
---|---|---|
Agathobacter rectalis | ||
Eubacterium |
Revision editor(s): Fatima
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoplasia free
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adenoma patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa between Adenoma patients and neoplasia free
Abundance in Group 1: decreased abundance in Adenoma patients
NCBI | Quality Control | Links |
---|---|---|
Ruminococcus |
Revision editor(s): Fatima
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoplasia free control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC
- Group 0 sample size Number of subjects in the control (unexposed) group
- 88
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure S3
Description: Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas)
Abundance in Group 1: increased abundance in CRC
Revision editor(s): Fatima
Signature 2
Source: Supplementary Figure S3
Description: Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas)
Abundance in Group 1: decreased abundance in CRC
Revision editor(s): Fatima