Dynamic microbe and molecule networks in a mouse model of colitis-associated 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
Empty strings are not accepted.
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS to induce chronic colitis and colorectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- 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).
- log transformation
- Statistical test
- edgeR
- 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)?
- Yes
Signature 1
Source: Table S2, Fig. 4B
Description: Differential OTUs between control mice and AOM/DSS-treated mice, showing significant microbial shifts associated with colorectal cancer progression.
Abundance in Group 1: increased abundance in AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Signature 2
Source: Table S2, Fig. 4B
Description: Differential OTUs between control mice and AOM/DSS-treated mice, showing significant microbial shifts associated with colorectal cancer progression.
Abundance in Group 1: decreased abundance in AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Experiment 2
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice with inflammation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice with dysplasia/cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that developed dysplasia and cancer and were treated with 3-4 AOM/DSS cycles
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S3
Description: OTUs distinguishing inflammation from colorectal cancer, highlighting taxa involved in cancer-related microbiome changes.
Abundance in Group 1: increased abundance in Mice with dysplasia/cancer
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Muribaculaceae |
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Signature 2
Source: Table S3
Description: Differential OTUs between mice with Inflammation and cancer
Abundance in Group 1: decreased abundance in Mice with dysplasia/cancer
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Experiment 3
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOM/DSS Cycle 1 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after treatment of different AOM/DSS cycles
Abundance in Group 1: increased abundance in AOM/DSS Cycle 1 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Signature 3
Source: Table S4
Description: Differential OTUs after treatment of different AOM/DSS cycles
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 1 group
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Prevotella | ||
| Mediterraneibacter gnavus |
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Experiment 4
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOM/DSS Cycle 2 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after 2 cycles of AOM/DSS treatment, showing intermediate changes in the gut microbiota.
Abundance in Group 1: increased abundance in AOM/DSS Cycle 2 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differential OTUs after 2 cycles of AOM/DSS treatment, showing intermediate changes in the gut microbiota.
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 2 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Experiment 5
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOM/DSS Cycle 3 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after 3 cycles of AOM/DSS treatment, indicating microbial changes at advanced disease stages.
Abundance in Group 1: increased abundance in AOM/DSS Cycle 3 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differential OTUs after 3 cycles of AOM/DSS treatment, indicating microbial changes at advanced disease stages.
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 3 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Experiment 6
Empty strings are not accepted.
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOM/DSS Cycle 4 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 4
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after 4 cycles of AOM/DSS treatment, representing microbiota alterations during late-stage colorectal cancer.
Abundance in Group 1: increased abundance in AOM/DSS Cycle 4 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differential OTUs after 4 cycles of AOM/DSS treatment, representing microbiota alterations during late-stage colorectal cancer.
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 4 group
Revision editor(s): Wendy640, KateRasheed, WikiWorks
