Gut mucosal microbiome across stages of colorectal carcinogenesis/Experiment 5
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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31
Curated date: 2022/06/25
Curator: Jeshudy
Revision editor(s): WikiWorks, Claregrieve1, Jeshudy, Victoria
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
- Intestine Bowel,Intestinal tract,Intestine,intestine
- 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
- adenoma-adjacent
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adenocarcinoma mucosae
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- specimens collected from adenocarcinoma tissue
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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
- Matched on: "subject" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.subject
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31
Source: Supplementary Figure 9
Description: Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples
Abundance in Group 1: decreased abundance in adenocarcinoma mucosae
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus sp. (in: firmicutes) | ||
| Enhydrobacter sp. | ||
| Escherichia coli | ||
| Pedobacter cryoconitis | ||
| Pseudomonas veronii | ||
| Rothia terrae |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31
Source: Supplementary Figure 9
Description: Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples
Abundance in Group 1: increased abundance in adenocarcinoma mucosae
Revision editor(s): Jeshudy, Claregrieve1
