Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models/Experiment 1
Curated date: 2022/01/21
Curator: Itslanapark
Revision editor(s): Itslanapark, WikiWorks, Peace Sandy
Subjects
- 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
- Non disease controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with colorectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 632
- Group 1 sample size Number of subjects in the case (exposed) group
- 354
Lab analysis
- Sequencing type
- 16S
- 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
- Mann-Whitney (Wilcoxon)
- 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
- 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
- unchanged
Signature 1
Source: Figure 1
Description: Disease-specific and shared microbial markers showed distinct prevalence profiles in patients and controls. (A) Microbial markers and their trends (i.e., case- or control-enriched) in common intestinal diseases. Species significantly enriched in cases (or controls) of corresponding disease in meta-analysis are shown (fdr < 0.05 in meta-analysis, Benjamini-Hochberg FDR correction), with their phylum shown on top. Red indicates case-enriched species and blue indicates control-enriched ones.
Abundance in Group 1: decreased abundance in CRC patients
Revision editor(s): Itslanapark, Peace Sandy
Signature 2
Curated date: 2022/01/25
Curator: Itslanapark
Revision editor(s): Itslanapark, Aiyshaaaa, Peace Sandy
Source: Figure 1
Description: Disease-specific and shared microbial markers showed distinct prevalence profiles in patients and controls. (A) Microbial markers and their trends (i.e., case- or control-enriched) in common intestinal diseases. Species significantly enriched in cases (or controls) of corresponding disease in meta-analysis are shown (fdr < 0.05 in meta-analysis, Benjamini-Hochberg FDR correction), with their phylum shown on top. Red indicates case-enriched species and blue indicates control-enriched ones.
Abundance in Group 1: increased abundance in CRC patients
Revision editor(s): Itslanapark, Aiyshaaaa, Peace Sandy
