Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing/Experiment 1
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Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Curated date: 2022/01/31
Curator: Itslanapark
Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Peace Sandy
Subjects
- Location of subjects
- France
- United States of America
- 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 carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pre treatment colorectal cancer cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 94
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
- Sequencing type
- 16S
- 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).
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- body mass index, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Signature 1
Needs review
Curated date: 2022/02/03
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Source: Table 3
Description: Differential microbial abundance between CRC cases and controls using 16S sequencing
Abundance in Group 1: decreased abundance in CRC cases
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Coprococcus | ||
| Lachnospiraceae |
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
