Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-19
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
- Mismatch repair cancer syndrome Mismatch repair cancer syndrome,mismatch repair cancer syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- proficient DNA mismatch repair (pMMR) CRC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- deficient DNA mismatch repair (dMMR) CRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- dMMR in colorectal cancer (CRC) characterized by robust immune environment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 207
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
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).
- raw counts
- Statistical test
- Linear Regression
- 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
- 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
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-19
Source: Table S2, Figure 2c
Description: Differential microbial abundance between deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) in CRC
Abundance in Group 1: increased abundance in deficient DNA mismatch repair (dMMR) CRC
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-19
Source: Table S2
Description: Differential microbial abundance between deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) in CRC
Abundance in Group 1: decreased abundance in deficient DNA mismatch repair (dMMR) CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Flavonifractor plautii | ||
| Gemella haemolysans |
Revision editor(s): ChiomaBlessing
