Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers/Experiment 3
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
- 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 (CTRL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- proficient DNA mismatch repair (pMMR) CRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pMMR in colorectal cancer (CRC) characterized by immunosuppressive tumor microenvironment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 227
- Group 1 sample size Number of subjects in the case (exposed) group
- 207
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
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-19
Source: Figure 2c
Description: Differential microbial abundance between proficient DNA mismatch repair (pMMR) in CRC and healthy controls (CTRL)
Abundance in Group 1: increased abundance in proficient DNA mismatch repair (pMMR) CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Flavonifractor plautii |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-19
Source: Figure 2c
Description: Differential microbial abundance between proficient DNA mismatch repair (pMMR) in CRC and healthy controls (CTRL)
Abundance in Group 1: decreased abundance in proficient DNA mismatch repair (pMMR) CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotignum propionicum | ||
| Collinsella aerofaciens | ||
| Gordonibacter pamelaeae |
Revision editor(s): ChiomaBlessing
