The human gut microbiome as a screening tool for 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
Subjects
- Location of subjects
- Canada
- 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
- 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 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
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- carcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with colonic adenocarcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 2.5
Signature 1
Source: Supplemental Figure 2 and text
Description: LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.
Abundance in Group 1: increased abundance in carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Fusobacterium | ||
| Lachnospiraceae | ||
| Porphyromonas | ||
| Clostridium | ||
| Porphyromonadaceae |
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Supplemental Figure 2 and text
Description: LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.
Abundance in Group 1: decreased abundance in carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Eubacteriales | ||
| Lachnospiraceae | ||
| Staphylococcus | ||
| Clostridium |
Revision editor(s): WikiWorks, Peace Sandy
Experiment 2
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- Adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with colonic adenoma
Lab analysis
Statistical Analysis
Signature 1
Source: Supplemental Figure 1
Description: LeFSe analysis for healthy vs. adenoma clinical groups. LDA values are represented for OTUs enriched in healthy and adenoma clinical groups.
Abundance in Group 1: increased abundance in Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Porphyromonadaceae | ||
| Pseudomonas |
Revision editor(s): Peace Sandy, WikiWorks
Signature 2
Source: Supplemental Figure 1
Description: LeFSe analysis for healthy vs. adenoma clinical groups. LDA values are represented for OTUs enriched in healthy and adenoma clinical groups.
Abundance in Group 1: decreased abundance in Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Clostridium | ||
| Lachnospiraceae | ||
| Odoribacter |
Revision editor(s): Peace Sandy, WikiWorks
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colonic lesions
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Combination of the clinical and microbiome data from adenoma and carcinoma subjects to create a combined colonic lesion group.
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
Lab analysis
Statistical Analysis
Signature 1
Source: Supplemental Figure 3
Description: LeFSe analysis for healthy vs. colonic lesion clinical groups. Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group). LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.
Abundance in Group 1: increased abundance in Colonic lesions
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonadaceae | ||
| Pseudomonas |
Revision editor(s): Peace Sandy, WikiWorks
Signature 2
Source: Supplemental Figure 3.
Description: LeFSe analysis for healthy vs. colonic lesion clinical groups. Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group). LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.
Abundance in Group 1: decreased abundance in Colonic lesions
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lachnospiraceae | ||
| Clostridium |
Revision editor(s): Peace Sandy, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adenoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Carcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with colonic adenocarcinoma
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Signature 1
Source: Supplemental Figure 4.
Description: LeFSe analysis for adenoma vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in adenoma and carcinoma clinical groups.
Abundance in Group 1: increased abundance in Carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Clostridium | ||
| Fusobacterium | ||
| Parasutterella | ||
| Phascolarctobacterium | ||
| Porphyromonas |
Revision editor(s): Peace Sandy, WikiWorks
Signature 2
Source: Supplemental Figure 4
Description: LeFSe analysis for adenoma vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in adenoma and carcinoma clinical groups.
Abundance in Group 1: decreased abundance in Carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Lachnospiraceae | ||
| Ruminococcus | ||
| Clostridium |
Revision editor(s): Peace Sandy, WikiWorks
