Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer/Experiment 3
From BugSigDB
Subjects
- Location of subjects
- South Korea
- 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
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to platinum-based neoadjuvant chemotherapy Response to platinum-based neoadjuvant chemotherapy,response to platinum-based neoadjuvant chemotherapy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-nCRT (Pre-neoadjuvant chemoradiotherapy)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-nCRT (Post-neoadjuvant chemoradiotherapy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients during post-neoadjuvant chemoradiotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3A
Description: Differentially abundant taxa before and after nCRT: red nodes indicate increased abundance post-nCRT; green nodes show decreased abundance
Abundance in Group 1: increased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy)
Revision editor(s): Tosin
Signature 2
Source: Figure 3A
Description: Differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) : red nodes indicate increased abundance post-nCRT (Neo-adjuvant chemoradiotherapy) : green nodes show decreased abundance
Abundance in Group 1: decreased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy)
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonadaceae | ||
| Aeromonadales | ||
| Aeromonas | ||
| Alloprevotella | ||
| Bacteroidaceae | ||
| Bacteroidales | ||
| Bacteroides | ||
| Eubacteriales | ||
| Lachnospiraceae | ||
| Prevotella | ||
| Prevotellaceae |
Revision editor(s): Tosin
