Edit Experiment: Study 717/Experiment 2

From BugSigDB

You do not have permission to edit this page, for the following reason:

The action you have requested is limited to users in the group: Users.


Location of subjects: Country from which study subjects were recruited
Host species: Species from which microbiome was sampled. Contact us to have more species added.
Body site: Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Find a term
Use a semicolon as the multiple values delimiter.
Condition: The experimental condition / phenotype studied according to the Experimental Factor Ontology
Find a term
Use a semicolon as the multiple values delimiter.
Group 0 name: Corresponds to the control (unexposed) group for case-control studies
Group 1 name: Corresponds to the case (exposed) group for case-control studies
Group 1 definition: Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Group 0 sample size: Number of subjects in the control (unexposed) group
Group 1 sample size: Number of subjects in the case (exposed) group
Antibiotics exclusion: Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

Lab analysis

Sequencing type: Experimental technique used for quantifying microbial abundance
16S variable region (lower bound): V
16S variable region (upper bound - only set if needed): V
Sequencing platform: Manufacturer and experimental platform used for quantifying microbial abundance

Statistical Analysis

Data transformation: Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Statistical test: Statistical test or computational tool used for differential abundance testing
Significance threshold: p-value or FDR threshold used for differential abundance testing (if any)
MHT correction: Have statistical tests be corrected for multiple hypothesis testing (MHT)?
LDA Score above: Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Matched on: Factors on which subjects have been matched on in a case-control study
Confounders controlled for: Confounding factors that have been accounted for by stratification or model adjustment

Alpha Diversity

Pielou: Quantifies how equal the community is numerically
Shannon: Estimator of species richness and species evenness: more weight on species richness
Chao1: Abundance-based estimator of species richness
Simpson: Estimator of species richness and species evenness: more weight on species evenness
Inverse Simpson: Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
Richness: Number of species
Faith: Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

Form data

This form's data is: Mark as incomplete to complete the form at a later time. Mark as complete to submit the page to a reviewer.