Identification of colorectal cancer progression-associated intestinal microbiome and predictive signature construction
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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
- 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 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
- Low CRC in stage I-II
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High CRC in stage III-IV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The relationship between intestinal microbiome and colorectal cancer (CRC) progression
- Group 0 sample size Number of subjects in the control (unexposed) group
- 62
- Group 1 sample size Number of subjects in the case (exposed) group
- 130
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- one 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).
- raw counts
- Statistical test
- Chi-Square
- Pearson Correlation
- Spearman Correlation
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.003
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- colorectal cancer
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Alpha diversity details is in figure 1
Description: The abundance and diversity of intestinal microbiome may increase taxa gradually with the occurrence and progression of CRC. increased fetal abundance of Proteus, Parabacteroides, Alistipes and Ruminococcus may contribute to CRC progression. Enhanced synthesis of O - glycans may result in CRC progression. Alistipes indistinctus may play a facilitated role in mast cell maturation by boosting IL-6 production. Alistipes indistinctus may work in the correct folding of endoplasmic reticulum proteins in CRC, reducing ER stress and prompting the survival and deterioration of CRC, which may owe to the enhanced PERK expression and activation of downstream UPR by Alistipes indistinctus. The CRC progression-associated differential intestinal microbiome identified as potential microbial markers for CRC staging prediction.
Abundance in Group 1: increased abundance in High CRC in stage III-IV
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Alistipes indistinctus | ||
| Parabacteroides | ||
| Ruminococcus | ||
| Proteus |
Revision editor(s): Oladoye
Signature 2
Source: Alpha diversity details is in figure 1
Description: The abundance and diversity of intestinal microbiome may increase taxa gradually with the occurrence and progression of CRC. increased fetal abundance of Proteus, Parabacteroides, Alistipes and Ruminococcus may contribute to CRC progression. Enhanced synthesis of O - glycans may result in CRC progression. Alistipes indistinctus may play a facilitated role in mast cell maturation by boosting IL-6 production. Alistipes indistinctus may work in the correct folding of endoplasmic reticulum proteins in CRC, reducing ER stress and prompting the survival and deterioration of CRC, which may owe to the enhanced PERK expression and activation of downstream UPR by Alistipes indistinctus. The CRC progression-associated differential intestinal microbiome identified as potential microbial markers for CRC staging prediction.
Abundance in Group 1: decreased abundance in High CRC in stage III-IV
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Oladoye
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low CRC in stage I-II high
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Identification of intestinal microbiome associated with CRC progression, LDA Effect Size (LEfSe) analysis on fecal microbiota of CRC patients with stage I-II and III-IV respectively.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Linear Discriminant Analysis
- 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)?
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 10
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Figure 2
Description: Identification of intestinal microbiome associated with CRC progression and potential biomarkers of intestinal microbiome associated with CRC progression, LDA Effect Size (LEfSe) analysis on fecal microbiota of CRC patients with stage I-II and III-IV respectively
Abundance in Group 1: increased abundance in High CRC in stage III-IV
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Butyricicoccus | ||
| Parabacteroides | ||
| Sporobacter |
Revision editor(s): Oladoye
Signature 2
Source: Figure 2
Description: Identification of intestinal microbiome associated with CRC progression and potential biomarkers of intestinal microbiome associated with CRC progression, LDA Effect Size (LEfSe) analysis on fecal microbiota of CRC patients with stage I-II and III-IV respectively
Abundance in Group 1: decreased abundance in High CRC in stage III-IV
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria |
Revision editor(s): Oladoye
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low CRC in stage I-II
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Relationship between CRC progression-associated microbiota and tumor-infiltrating immune cells
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- Pearson Correlation
- Spearman Correlation
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- colorectal cancer
Signature 1
Source: Figure 4
Description: Correlation of CRC progression-related differential intestinal flora with tumor immune infiltrating cells
Abundance in Group 1: increased abundance in High CRC in stage III-IV
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Alphaproteobacteria | ||
| Carnobacteriaceae | ||
| Dolosigranulum | ||
| Rhodospirillaceae | ||
| Rhodospirillales |
Revision editor(s): Oladoye
Signature 2
Source: Figure 4
Description: Correlation of CRC progression-related differential intestinal flora with tumor immune infiltrating cells
Abundance in Group 1: decreased abundance in High CRC in stage III-IV
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Butyricicoccus |
Revision editor(s): Oladoye
Experiment 4
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Identification of intestinal microbiome associated with CRC progression, LDA Effect Size (LEfSe) analysis of fecal microbiota of CRC patients with stage I-II and III-IV respectively.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Sequencing type
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Not specified
Statistical Analysis
- Statistical test
- LEfSe
- Linear Discriminant Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 10
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
