Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
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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
- Spain
- 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
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- 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
- Adjacent normal colonic tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colon Tumor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor tissues with colorectal carcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
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
- 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
- 1.8
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 1C
Description: Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by whole-genome sequencing in nine individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).
Abundance in Group 1: increased abundance in Colon Tumor
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium nucleatum | ||
| Streptococcaceae | ||
| Aggregatibacter | ||
| Aggregatibacter aphrophilus |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 1C
Description: Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by whole-genome sequencing in nine individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).
Abundance in Group 1: decreased abundance in Colon Tumor
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter cloacae | ||
| Enterobacter | ||
| Acinetobacter baumannii | ||
| Acinetobacter | ||
| Acinetobacter sp. |
Revision editor(s): MyleeeA
Experiment 2
Subjects
- Group 0 sample size Number of subjects in the control (unexposed) group
- 95
- Group 1 sample size Number of subjects in the case (exposed) group
- 95
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.2
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 2C
Description: Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by 16S rDNA sequencing in 95 individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).
Abundance in Group 1: increased abundance in Colon Tumor
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacteriales | ||
| Fusobacterium | ||
| Fusobacteriia |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2C
Description: Linear discriminant analysis (LDA) coupled with effect size measurements identifies Fusobacterium as the most differentially abundant taxon in colon tumor versus normal specimens by 16S rDNA sequencing in 95 individuals. Tumor-enriched taxa are indicated with a positive LDA score (black), and taxa enriched in normal tissue have a negative score (gray).
Abundance in Group 1: decreased abundance in Colon Tumor
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Bacteroides | ||
| Bacteroidaceae | ||
| Oscillospiraceae | ||
| Bacteroidia | ||
| Bacteroidales | ||
| Eubacteriales | ||
| Clostridia | ||
| Bacillota |
Revision editor(s): MyleeeA
